count: 19509
list:
- accessibility: Open access
  additionDate: '2026-06-14T08:34:19.506926Z'
  biotoolsCURIE: biotools:phylo-movies
  biotoolsID: phylo-movies
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: enes@lbi-netmed.at
    fundrefid: null
    gridid: null
    name: Enes Berk Sakalli
    note: Corresponding software contact.
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: https://github.com/enesBerkSakalli
  - email: null
    fundrefid: null
    gridid: null
    name: Simon E. Haendeler
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Arndt von Haeseler
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Heiko A. Schmidt
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: Phylo-Movies is an open-source React and Flask web application, also
    available as a desktop app, for inspecting ordered phylogenetic tree series. It
    computes and visualizes subtree-prune-and-regraft transition frames between consecutive
    trees, helping users see which taxa or subtrees move across sliding-window analyses,
    bootstrap replicates, and curated tree-series comparisons. The viewer includes
    timeline playback, tree comparison, MSA context, coloring, analytics, image export,
    and recording tools.
  documentation:
  - note: Researcher-facing manual.
    type:
    - User manual
    url: https://enesberksakalli.github.io/phylo-movies/manual/
  - note: Project overview, installation, usage, citation, and links.
    type:
    - General
    url: https://github.com/enesBerkSakalli/phylo-movies/blob/main/README.md
  - note: Local source-checkout setup instructions.
    type:
    - Installation instructions
    url: https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/getting-started.md
  - note: Backend API documentation.
    type:
    - API documentation
    url: https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/api.md
  download:
  - note: Source checkout for full web application and backend workflows.
    type: Source code
    url: https://github.com/enesBerkSakalli/phylo-movies
    version: 0.98.1
  - note: Desktop convenience builds for macOS, Windows, and Linux.
    type: Binaries
    url: https://github.com/enesBerkSakalli/phylo-movies/releases/tag/v0.98.1
    version: 0.98.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Visualizes ordered phylogenetic tree series as animated transition movies
      with comparison, MSA context, movement analytics, image export, and recording
      support.
    operation:
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    output:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://enesberksakalli.github.io/phylo-movies/
  homepage_status: 0
  language:
  - Python
  - JavaScript
  - TypeScript
  lastUpdate: '2026-06-14T08:36:42.066838Z'
  license: MIT
  link:
  - note: Source code repository.
    type:
    - Repository
    url: https://github.com/enesBerkSakalli/phylo-movies
  - note: Static browser demo with precomputed example movies.
    type:
    - Service
    url: https://enesberksakalli.github.io/phylo-movies/demo/
  - note: null
    type:
    - Issue tracker
    url: https://github.com/enesBerkSakalli/phylo-movies/issues
  maturity: Mature
  name: Phylo-Movies
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: enes
  publication:
  - doi: 10.64898/2026.04.01.715821
    metadata: null
    note: bioRxiv preprint describing the Phylo-Movies method and examples.
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.5281/zenodo.20488923
    metadata: null
    note: Archived software release on Zenodo.
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 0.98.1
  relation: []
  toolType:
  - Desktop application
  - Web application
  topic:
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version:
  - 0.98.1
- accessibility: Open access
  additionDate: '2026-06-12T15:37:36.437343Z'
  biotoolsCURIE: biotools:lacuna
  biotoolsID: lacuna
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: 'When a stroke, tumor, or other focal brain injury damages tissue,
    understanding its consequences requires placing the lesion within the broader
    organization of the brain. Lacuna is an open-source toolbox that uses normative
    reference data from healthy individuals, including connectivity datasets and anatomical
    atlases, to characterize lesions beyond their anatomical location.


    Users provide lesion masks in MNI space, and Lacuna automatically retrieves reference
    data, performs required processing steps, and generates BIDS-organized outputs.
    Designed for multicenter research, it standardizes workflows, scales from single
    cases to large cohorts, supports HPC deployment through containers, and records
    provenance for reproducible lesion analyses.'
  documentation:
  - note: null
    type:
    - Command-line options
    url: https://lacuna-py.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/m-petersen/lacuna
  homepage_status: 0
  language:
  - Python
  - Bash
  lastUpdate: '2026-06-12T15:37:45.183469Z'
  license: null
  link: []
  maturity: null
  name: Lacuna
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: marvin
  publication: []
  relation: []
  toolType: []
  topic:
  - term: Neurology
    uri: http://edamontology.org/topic_3334
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-08-01T11:05:01Z'
  biotoolsCURIE: biotools:proteinsplus
  biotoolsID: proteinsplus
  collectionID:
  - de.NBI
  - de.NBI-biodata
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: The ProteinsPlus web server aims to support life scientists in working
    with protein structures. Protein structures are the key to understanding protein
    function. They are an important resource in many biotechnological application
    areas from pharmaceutical research to biocatalysis. ProteinsPlus focuses on protein-ligand
    interactions. The server provides support for the initial steps of dealing with
    protein structures, namely structure search, quality assessment, and preprocessing.
    JAMDA enables users to perform an on-the-fly molecular docking of up to five molecules.
    The poses can then be visualized in 2D (PoseView, PoseEdit). Furthermore, advanced
    options, such as protein pocket detection (DoGSite), prediction of water molecule
    positions (WarPP), protein structure ensemble generation (SIENA), prediction of
    metal coordination (METALizer), the analysis of solvent channels in protein crystals
    (LifeSoaks), or the categorization of protein-protein-interfaces (HyPPI) are supported.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download: []
  editPermission:
    authors:
    - MelanieZBH
    - ehrt
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: prediction of protonation states and tautomers and placement of hydrogen
      atoms
    operation:
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: quality profiling for protein-ligand complexes
    operation:
    - term: Protein structure validation
      uri: http://edamontology.org/operation_0321
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    - term: Protein geometry validation
      uri: http://edamontology.org/operation_1844
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    output:
    - data:
        term: Protein structural quality report
        uri: http://edamontology.org/data_1539
      format: []
    - data:
        term: Protein geometry data
        uri: http://edamontology.org/data_2991
      format: []
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: calculating bottleneck radii for crystal solvent channels
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Accessible surface calculation
      uri: http://edamontology.org/operation_0384
    - term: Structure analysis
      uri: http://edamontology.org/operation_2480
    output:
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Map data
        uri: http://edamontology.org/data_2019
      format: []
    - data:
        term: Protein solvent accessibility
        uri: http://edamontology.org/data_1542
      format: []
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: atom-level assessment of the electron density fit for structures solved
      by X-ray crystallography
    operation:
    - term: Protein structure validation
      uri: http://edamontology.org/operation_0321
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Map data
        uri: http://edamontology.org/data_2019
      format: []
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: protein-protein interface classification (permanent, transient, crystal
      artifact)
    operation:
    - term: Protein-protein interaction analysis
      uri: http://edamontology.org/operation_2949
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    output:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: InChI
        uri: http://edamontology.org/format_1197
      - term: SMILES
        uri: http://edamontology.org/format_1196
      - term: Mol2
        uri: http://edamontology.org/format_3816
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: protein-ligand docking for small molecules
    operation:
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    - term: Salt bridge calculation
      uri: http://edamontology.org/operation_1839
    - term: Residue interaction calculation
      uri: http://edamontology.org/operation_0248
    - term: Protein-ligand docking
      uri: http://edamontology.org/operation_0482
    - term: Protein-metal contact calculation
      uri: http://edamontology.org/operation_1834
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    output:
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: small molecule binding site detection
    operation:
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    - term: Ligand-binding site prediction
      uri: http://edamontology.org/operation_3897
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Map data
        uri: http://edamontology.org/data_2019
      format: []
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: small molecule binding site detection and druggability assessment
    operation:
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    - term: Ligand-binding site prediction
      uri: http://edamontology.org/operation_3897
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    - data:
        term: Map data
        uri: http://edamontology.org/data_2019
      format: []
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: 2D interaction diagram drawing and editing
    operation:
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Salt bridge calculation
      uri: http://edamontology.org/operation_1839
    - term: Residue interaction calculation
      uri: http://edamontology.org/operation_0248
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    - term: Protein-metal contact calculation
      uri: http://edamontology.org/operation_1834
    output:
    - data:
        term: Protein-ligand interaction report
        uri: http://edamontology.org/data_1566
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Protein structure image
        uri: http://edamontology.org/data_2992
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Chemical structure image
        uri: http://edamontology.org/data_1712
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: metal complex geometry prediction
    operation:
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    - term: Protein-metal contact calculation
      uri: http://edamontology.org/operation_1834
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    output:
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: 2D interaction diagram drawing
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Salt bridge calculation
      uri: http://edamontology.org/operation_1839
    - term: Protein-metal contact calculation
      uri: http://edamontology.org/operation_1834
    - term: Residue interaction calculation
      uri: http://edamontology.org/operation_0248
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    output:
    - data:
        term: Protein-ligand interaction report
        uri: http://edamontology.org/data_1566
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
    - data:
        term: Chemical structure image
        uri: http://edamontology.org/data_1712
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
    - data:
        term: Protein structure image
        uri: http://edamontology.org/data_2992
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: structural single-residue substitution search and analysis
    operation:
    - term: Structure database search
      uri: http://edamontology.org/operation_0339
    - term: Pairwise structure alignment
      uri: http://edamontology.org/operation_0503
    - term: Local structure alignment
      uri: http://edamontology.org/operation_0509
    - term: Structural similarity search
      uri: http://edamontology.org/operation_0360
    output:
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
    - data:
        term: Protein structure alignment
        uri: http://edamontology.org/data_1481
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: PDB mining and protein binding site ensemble generation
    operation:
    - term: Structure clustering
      uri: http://edamontology.org/operation_2844
    - term: Simulation analysis
      uri: http://edamontology.org/operation_0244
    - term: Structural similarity search
      uri: http://edamontology.org/operation_0360
    - term: Structure database search
      uri: http://edamontology.org/operation_0339
    - term: Local structure alignment
      uri: http://edamontology.org/operation_0509
    - term: Pairwise structure alignment
      uri: http://edamontology.org/operation_0503
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Sequence alignment (protein)
        uri: http://edamontology.org/data_1384
      format: []
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Protein structure alignment
        uri: http://edamontology.org/data_1481
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: textual, numerical, and chemical 3D searches in the PDB
    operation:
    - term: Simulation analysis
      uri: http://edamontology.org/operation_0244
    - term: Text mining
      uri: http://edamontology.org/operation_0306
    - term: Structural similarity search
      uri: http://edamontology.org/operation_0360
    - term: Structure database search
      uri: http://edamontology.org/operation_0339
    - term: Local structure alignment
      uri: http://edamontology.org/operation_0509
    - term: Pairwise structure alignment
      uri: http://edamontology.org/operation_0503
    output:
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Protein structure alignment
        uri: http://edamontology.org/data_1481
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
  - cmd: null
    input:
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: water molecule placement
    operation:
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://proteins.plus
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T09:56:30.953754Z'
  license: Other
  link:
  - note: null
    type:
    - Service
    url: https://proteins.plus
  maturity: Mature
  name: ProteinsPlus
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1093/nar/gkx333
    metadata: null
    note: null
    pmcid: PMC5570178
    pmid: '28472372'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkaa235
    metadata: null
    note: null
    pmcid: PMC7319454
    pmid: '32297936'
    type:
    - Usage
    version: null
  - doi: 10.1093/nar/gkac305
    metadata: null
    note: null
    pmcid: PMC9252762
    pmid: '35489057'
    type:
    - Usage
    version: null
  - doi: 10.1093/nar/gkaf377
    metadata: null
    note: null
    pmcid: PMC12230695
    pmid: '40326518'
    type:
    - Usage
    version: null
  relation:
  - biotoolsID: dogsitescorer
    type: includes
  - biotoolsID: dogsite3
    type: includes
  - biotoolsID: edia
    type: includes
  - biotoolsID: siena
    type: includes
  - biotoolsID: metalizer
    type: includes
  - biotoolsID: structureprofiler
    type: includes
  - biotoolsID: jamda
    type: includes
  - biotoolsID: geomine
    type: includes
  - biotoolsID: microminer
    type: includes
  - biotoolsID: poseedit
    type: includes
  - biotoolsID: poseview
    type: includes
  - biotoolsID: protoss
    type: includes
  - biotoolsID: lifesoaks
    type: includes
  - biotoolsID: ppi
    type: includes
  toolType:
  - Web service
  - Web API
  topic:
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  validated: 1
  version: []
- accessibility: null
  additionDate: '2025-12-17T13:59:47.755840Z'
  biotoolsCURIE: biotools:microminer
  biotoolsID: microminer
  collectionID:
  - de.NBI-biodata
  - de.NBI
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: null
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
    gridid: null
    name: null
    note: Primary Contact for Standalone Tool Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: MicroMiner assists in identifying single-residue substitutions in protein
    structure databases. It searches protein residue environments with local sequence
    and structural similarity based on the SIENA methodology. Users can search for
    structural mutation in the entire PDB, their in-house structure collection, or
    (subsets of) the AlphaFold Database. They can use the method to explore the mutation
    landscape of proteins with experimental or predicted structures. MicroMiner can
    be applied to single domains or even protein-protein or protein-ligand interfaces.
    Several filter options to simplify downstream analysis are available.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download:
  - note: Please register to download the tool.
    type: Binaries
    url: https://uhh.de/naomi
    version: null
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: structural single-residue substitution search and analysis
    operation:
    - term: Pairwise structure alignment
      uri: http://edamontology.org/operation_0503
    - term: Structural similarity search
      uri: http://edamontology.org/operation_0360
    - term: Structure database search
      uri: http://edamontology.org/operation_0339
    - term: Local structure alignment
      uri: http://edamontology.org/operation_0509
    output:
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
    - data:
        term: Protein structure alignment
        uri: http://edamontology.org/data_1481
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/microminer.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T09:55:54.271765Z'
  license: Other
  link:
  - note: A web service to run MicroMiner calculations for protein structures stored
      in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded
      structures.
    type:
    - Service
    url: https://proteins.plus
  maturity: Mature
  name: MicroMiner
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1093/bib/bbad357
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: siena
    type: uses
  toolType:
  - Command-line tool
  - Web service
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Protein folding, stability and design
    uri: http://edamontology.org/topic_0130
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-12-17T13:44:30.421942Z'
  biotoolsCURIE: biotools:jamda
  biotoolsID: jamda
  collectionID:
  - de.NBI
  - de.NBI-biodata
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
    gridid: null
    name: NAOMI ChemBio Suite Support
    note: Primary Contact for Standalone Tool Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: JAMDA enables the preparation of individual protein structures and
    the docking of small molecules in preprocessed binding sites of choice. JAMDA
    simplifies the process of protein-ligand docking by automatic preprocessing protocols
    for the protein and binding sites of interest. The JAMDAscore scoring function
    retrieved 75% of the native poses in the three highest-ranked solutions for high-quality
    protein-ligand complexes with default settings. Individual configurations for
    protein preparation are available, e.g., considering protein ensembles, relevant
    binding site water molecules, or cofactors. A user-defined number of input conformations
    for the ligands of interest can be generated fully automated using Conformator.
    Alternatively, users can also provide externally prepared ligand conformers.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download:
  - note: Please register to download the tool.
    type: Binaries
    url: https://uhh.de/naomi
    version: null
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SMILES
        uri: http://edamontology.org/format_1196
      - term: Mol2
        uri: http://edamontology.org/format_3816
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: InChI
        uri: http://edamontology.org/format_1197
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: protein-ligand docking for small molecules
    operation:
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    - term: Protein-ligand docking
      uri: http://edamontology.org/operation_0482
    - term: Residue interaction calculation
      uri: http://edamontology.org/operation_0248
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    - term: Protein-metal contact calculation
      uri: http://edamontology.org/operation_1834
    - term: Salt bridge calculation
      uri: http://edamontology.org/operation_1839
    output:
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/jamda.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T09:54:09.726046Z'
  license: Other
  link:
  - note: A web service to run JAMDA calculations for protein structures stored in
      the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.
    type:
    - Service
    url: https://proteins.plus
  maturity: Mature
  name: JAMDA
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1021/acs.jcim.3c01573
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1002/jcc.26522
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  - doi: 10.1021/acs.jcim.0c01095
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  relation:
  - biotoolsID: protoss
    type: uses
  toolType:
  - Web service
  - Command-line tool
  topic:
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-01-18T10:36:05Z'
  biotoolsCURIE: biotools:geomine
  biotoolsID: geomine
  collectionID:
  - de.NBI
  - de.NBI-biodata
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: GeoMine enables the automated mining of protein-ligand binding sites.
    Based on individually designed queries, users can search for spatial interaction
    patterns in huge collections of protein-ligand complexes and binding pockets.
    The regularly updated GeoMine database relies on the free database systems SQLite
    and PostgreSQL. It supports radius-based pockets (based on ligands and predicted
    pockets (based on DoGSite3) for query generation. The query management is based
    on XML (for the REST service) or JSON in the GUI mode. Its output consists of
    the query-based superpositions of the matched binding sites and statistics on
    matching points, distances, and angles.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download: []
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: textual, numerical, and chemical 3D searches in the PDB
    operation:
    - term: Simulation analysis
      uri: http://edamontology.org/operation_0244
    - term: Text mining
      uri: http://edamontology.org/operation_0306
    - term: Structural similarity search
      uri: http://edamontology.org/operation_0360
    - term: Structure database search
      uri: http://edamontology.org/operation_0339
    - term: Local structure alignment
      uri: http://edamontology.org/operation_0509
    - term: Pairwise structure alignment
      uri: http://edamontology.org/operation_0503
    output:
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Protein structure alignment
        uri: http://edamontology.org/data_1481
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
  homepage: https://www.zbh.uni-hamburg.de/forschung/amd/software/geomine.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T09:52:43.985500Z'
  license: Other
  link:
  - note: A web service to run GeoMine calculations for protein structures stored
      in the Protein Data Bank and AlphaFold Protein Structure Database.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run GeoMine calculations for protein structures stored in the
      Protein Data Bank and AlphaFold Protein Structure Database.
    type:
    - Service
    url: https://proteins.plus/help/geomine_rest
  maturity: Mature
  name: GeoMine
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1093/bioinformatics/btaa693
    metadata: null
    note: null
    pmcid: null
    pmid: '32735322'
    type:
    - Usage
    version: null
  - doi: 10.1021/acs.jcim.6b00561
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  - doi: 10.1021/acs.jmedchem.1c01046
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1007/s10822-024-00563-3
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Usage
    version: null
  relation:
  - biotoolsID: dogsite3
    type: uses
  - biotoolsID: protoss
    type: uses
  toolType:
  - Web service
  - Web API
  topic:
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  validated: 1
  version: []
- accessibility: null
  additionDate: '2019-07-06T06:35:25Z'
  biotoolsCURIE: biotools:StructureProfiler
  biotoolsID: StructureProfiler
  collectionID:
  - de.NBI
  - de.NBI-biodata
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
    gridid: null
    name: NAOMI ChemBio Suite Support
    note: Primary Contact for Standalone Tool Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: Three-dimensional protein structures play a vital role in drug design.
    Structure-based design necessitates an in-depth examination of the available quality
    data before using the structure in computational experiments and for method evaluation.
    StructureProfiler assists in automatically profiling sets of protein-ligand complex
    structures based on multiple quality indicators, ranging from model characteristics,
    e.g., the R factor, and active site features, e.g., bond length deviations, to
    ligand properties such as electron density support and the validity of torsion
    angles.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download:
  - note: null
    type: Binaries
    url: https://uhh.de/naomi
    version: null
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: quality profiling for protein-ligand complexes
    operation:
    - term: Protein structure validation
      uri: http://edamontology.org/operation_0321
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    - term: Protein geometry validation
      uri: http://edamontology.org/operation_1844
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    output:
    - data:
        term: Protein structural quality report
        uri: http://edamontology.org/data_1539
      format: []
    - data:
        term: Protein geometry data
        uri: http://edamontology.org/data_2991
      format: []
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/structureprofiler.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T09:50:59.800180Z'
  license: Other
  link:
  - note: A web service to run StructureProfiler calculations for protein structures
      stored in the Protein Data Bank.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run StructureProfiler calculations for protein structures stored
      in the Protein Data Bank.
    type:
    - Service
    url: https://proteins.plus/help/structurechecker_rest
  - note: Link to download the standalone tool from the NAOMI ChemBio Suite.
    type:
    - Software catalogue
    url: https://uhh.de/naomi
  maturity: Mature
  name: StructureProfiler
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1093/bioinformatics/bty692
    metadata: null
    note: null
    pmcid: null
    pmid: '30124779'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web service
  - Web API
  - Command-line tool
  topic:
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Structural biology
    uri: http://edamontology.org/topic_1317
  validated: 1
  version: []
- accessibility: null
  additionDate: '2020-06-08T16:17:43Z'
  biotoolsCURIE: biotools:warpp
  biotoolsID: warpp
  collectionID:
  - de.NBI-biodata
  - de.NBI
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
    gridid: null
    name: NAOMI ChemBio Suite Support
    note: Primary Contact for Standalone Tool Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: WarPP predicts the position and orientation of water molecules in small-molecule
    binding sites. It places and scores water molecules in binding sites of crystallographic
    structures based on EDIAscorer results and interaction geometries as known from
    experimentally solved protein structures. WarPP was validated on a high-quality
    set of 1,500 protein-ligand complexes, containing 20,000 crystallographically
    observed water molecules. It is sufficiently fast for high-throughput analyses.
    It correctly places water molecules in approx. 80% of the cases. Users can export
    the predictions as PDB files for, e.g., molecular docking with JAMDA.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download:
  - note: null
    type: Binaries
    url: https://uhh.de/naomi
    version: null
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: water molecule placement
    operation:
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://www.zbh.uni-hamburg.de/forschung/amd/software/warpp.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T09:49:28.516069Z'
  license: Other
  link:
  - note: A web service to run WarPP calculations for protein structures stored in
      the Protein Data Bank.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run WarPP calculations for protein structures stored in the
      Protein Data Bank.
    type:
    - Service
    url: https://proteins.plus/help/warpp_rest
  - note: Link to download the standalone tool from the NAOMI ChemBio Suite.
    type:
    - Software catalogue
    url: https://uhh.de/naomi
  maturity: Mature
  name: WarPP
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1021/acs.jcim.8b00271
    metadata: null
    note: null
    pmcid: null
    pmid: '30036062'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web API
  - Web service
  topic:
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Structural biology
    uri: http://edamontology.org/topic_1317
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  validated: 1
  version: []
- accessibility: null
  additionDate: '2025-12-15T10:42:55.566760Z'
  biotoolsCURIE: biotools:lifesoaks
  biotoolsID: lifesoaks
  collectionID:
  - de.NBI
  - de.NBI-biodata
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
    gridid: null
    name: NAOMI ChemBio Suite Support
    note: Primary Contact for Standalone Tool Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: LifeSoaks was designed to find solvent channels in macromolecular structures
    solved by X-ray crystallography. It predicts their accessibility by molecules
    through an automated annotation of so-called bottleneck radii. It simplifies the
    process of manually checking a crystal structure for solvent channels. Bottleneck
    radii can be calculated for solvent channels and small molecule binding sites.
    The tool is ideally suited for channel analyses before the actual soaking experiments
    to select the most promising experimental conditions and crystal forms. LifeSoaks
    runs fully automated and will finish within seconds to minutes for moderately
    sized crystals.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download:
  - note: Please register to download the tool.
    type: Binaries
    url: https://uhh.de/naomi
    version: null
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: calculating bottleneck radii for crystal solvent channels
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Accessible surface calculation
      uri: http://edamontology.org/operation_0384
    - term: Structure analysis
      uri: http://edamontology.org/operation_2480
    output:
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Map data
        uri: http://edamontology.org/data_2019
      format: []
    - data:
        term: Protein solvent accessibility
        uri: http://edamontology.org/data_1542
      format: []
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/lifesoaks.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T09:48:27.447329Z'
  license: Other
  link:
  - note: A web service to run LifeSoaks calculations for protein structures stored
      in the Protein Data Bank.
    type:
    - Service
    url: https://proteins.plus
  - note: A link to download the standalone tool from the NAOMI ChemBio Suite.
    type:
    - Software catalogue
    url: https://uhh.de/naomi.de
  maturity: Mature
  name: LifeSoaks
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1107/S205979832300582X
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web service
  - Command-line tool
  topic:
  - term: X-ray diffraction
    uri: http://edamontology.org/topic_2828
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: null
  additionDate: '2020-06-08T16:00:55Z'
  biotoolsCURIE: biotools:metalizer
  biotoolsID: metalizer
  collectionID:
  - de.NBI
  - de.NBI-biodata
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: METALizer predicts the coordination geometry of metal ions in metalloproteins.
    Users can compare potential coordination geometries to those found in the examined
    structure. The predicted coordination geometries and the observed metal interaction
    distances can be interactively compared to statistics calculated based on the
    PDB.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download: []
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: metal complex geometry prediction
    operation:
    - term: Protein-metal contact calculation
      uri: http://edamontology.org/operation_1834
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    output:
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/metalizer.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T09:46:46.572015Z'
  license: Other
  link:
  - note: A web service to run METALizer calculations for protein structures stored
      in the Protein Data Bank.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run METALizer calculations for protein structures stored in
      the Protein Data Bank.
    type:
    - Service
    url: https://proteins.plus/help/metalizer_rest
  maturity: Mature
  name: METALizer
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1093/nar/gkaa235
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web service
  - Web API
  topic:
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-11-28T10:07:17Z'
  biotoolsCURIE: biotools:edia
  biotoolsID: edia
  collectionID:
  - de.NBI
  - de.NBI-biodata
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
    gridid: null
    name: NAOMI ChemBio Suite Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: null
    typeRole:
    - Provider
    url: null
  description: The electron density score for individual atoms (EDIA) quantifies the
    electron density fit of each atom in a crystallographically resolved structure.
    Multiple EDIA values can be combined using the power mean to compute the EDIAm,
    i.e., the electron density score for a group of several atoms. It enables users
    to score a set of atoms, such as a ligand, a residue, or an active site.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download:
  - note: null
    type: Binaries
    url: https://uhh.de/naomi
    version: null
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: atom-level assessment of the electron density fit for structures solved
      by X-ray crystallography
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    - term: Protein structure validation
      uri: http://edamontology.org/operation_0321
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Map data
        uri: http://edamontology.org/data_2019
      format: []
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/ediascorer.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T09:03:09.568414Z'
  license: Other
  link:
  - note: A web service to run EDIAscorer calculations for protein structures stored
      in the Protein Data Bank.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run EDIAscorer calculations for protein structures stored in
      the Protein Data Bank.
    type:
    - Service
    url: https://proteins.plus/help/edia_rest
  - note: A link to download the standalone tool from the NAOMI ChemBio Suite.
    type:
    - Software catalogue
    url: https://uhh.de/naomi
  maturity: Mature
  name: EDIAscorer
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1021/acs.jcim.7b00391
    metadata: null
    note: null
    pmcid: null
    pmid: '28981269'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: structureprofiler
    type: usedBy
  toolType:
  - Web service
  - Command-line tool
  - Web API
  topic:
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: X-ray diffraction
    uri: http://edamontology.org/topic_2828
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-11-28T10:07:16Z'
  biotoolsCURIE: biotools:ppi
  biotoolsID: ppi
  collectionID:
  - de.NBI
  - de.NBI-biodata
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: HyPPI classifies a protein-protein complex based on its interaction
    type into permanent, transient, or crystal artifact. Permanent protein-protein
    complexes are only stable in their complexed state. Their subunits would denature
    upon dissociation of the protein-protein complex. Transient protein-protein complexes
    are stable in the complexed as well as in the monomeric form, depending on the
    necessary function of the complex. Crystal artifacts have no biological function
    and are artificially formed during the crystallization process. The discrimination
    is performed using two characteristics of the protein-protein complex, the hydrophobicity
    of the interface (ΔGhydrophobic) and the quotient of interface area ratios (IF-quotient).
    The IF-quotient considers whether the protein-protein interface is symmetric.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download: []
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: protein-protein interface classification (permanent, transient, crystal
      artifact)
    operation:
    - term: Protein-protein interaction analysis
      uri: http://edamontology.org/operation_2949
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    output:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
  homepage: https://proteins.plus/help/ppi
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T09:01:12.035524Z'
  license: Other
  link:
  - note: A web service to run HyPPI calculations for protein structures stored in
      the Protein Data Bank or uploaded structures.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run HyPPI calculations for protein structures stored in the
      Protein Data Bank or uploaded structures.
    type:
    - Service
    url: https://proteins.plus/help/ppi_rest
  maturity: Legacy
  name: HyPPI
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1007/s10822-012-9626-2
    metadata: null
    note: null
    pmcid: null
    pmid: '23269578'
    type:
    - Method
    version: null
  - doi: 10.1093/nar/gkx333
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    - Usage
    version: null
  relation: []
  toolType:
  - Web service
  - Web API
  topic:
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-11-28T10:07:17Z'
  biotoolsCURIE: biotools:siena
  biotoolsID: siena
  collectionID:
  - de.NBI
  - de.NBI-biodata
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
    gridid: null
    name: NAOMI ChemBio Suite Support
    note: Primary Contact for Standalone Tool Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: SIENA is a software pipeline enabling the fully automated construction
    of protein structure ensembles from the PDB. Starting with a single query structure,
    all binding sites with high sequence similarity are extracted from the PDB, aligned,
    and superimposed. SIENA also handles complicated cases, such as comparing binding
    sites at protein domain interfaces or within multimeric proteins.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download:
  - note: Please register to download the tool.
    type: Binaries
    url: https://uhh.de/naomi
    version: null
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: PDB mining and protein binding site ensemble generation
    operation:
    - term: Structure clustering
      uri: http://edamontology.org/operation_2844
    - term: Simulation analysis
      uri: http://edamontology.org/operation_0244
    - term: Structural similarity search
      uri: http://edamontology.org/operation_0360
    - term: Structure database search
      uri: http://edamontology.org/operation_0339
    - term: Local structure alignment
      uri: http://edamontology.org/operation_0509
    - term: Pairwise structure alignment
      uri: http://edamontology.org/operation_0503
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Sequence alignment (protein)
        uri: http://edamontology.org/data_1384
      format: []
    - data:
        term: Root-mean-square deviation
        uri: http://edamontology.org/data_1497
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    - data:
        term: Protein structure alignment
        uri: http://edamontology.org/data_1481
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/siena.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T08:59:19.128862Z'
  license: Other
  link:
  - note: A web service to run SIENA calculations for protein structures stored in
      the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run SIENA calculations for protein structures stored in the
      Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.
    type:
    - Service
    url: https://proteins.plus/help/siena_rest
  - note: A link to download the standalone tool from the NAOMI ChemBio Suite.
    type:
    - Software catalogue
    url: https://uhh.de/naomi
  maturity: Mature
  name: SIENA
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1021/acs.jcim.5b00588
    metadata: null
    note: null
    pmcid: null
    pmid: '26759067'
    type:
    - Method
    - Primary
    version: null
  - doi: 10.1021/acs.jcim.5b00210
    metadata: null
    note: null
    pmcid: null
    pmid: '26098831'
    type:
    - Method
    version: null
  relation:
  - biotoolsID: proteinsplus
    type: includedIn
  toolType:
  - Web service
  - Web API
  - Command-line tool
  topic:
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  validated: 1
  version: []
- accessibility: null
  additionDate: '2025-12-15T10:27:32.766629Z'
  biotoolsCURIE: biotools:poseedit
  biotoolsID: poseedit
  collectionID:
  - de.NBI
  - de.NBI-biodata
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: PoseEdit automatically generates 2D diagrams of protein-ligand complexes,
    focusing on the interactions between protein and ligand. Interactions between
    molecules are estimated by an underlying interaction model that relies on atom
    types and simple geometric criteria. The structure mining tool GeoMine also uses
    this model to describe binding sites. In addition, users can manipulate the diagrams
    by translating, rotating, mirroring parts of the structure, adding additional
    interactions, or removing them. Furthermore, users can add individual labels or
    adjust available labels. Users can download the final 2D diagrams for a binding
    site of interest in JSON or SVG format.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download: []
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: 2D interaction diagram drawing and editing
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    - term: Residue interaction calculation
      uri: http://edamontology.org/operation_0248
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    - term: Protein-metal contact calculation
      uri: http://edamontology.org/operation_1834
    - term: Salt bridge calculation
      uri: http://edamontology.org/operation_1839
    output:
    - data:
        term: Protein-ligand interaction report
        uri: http://edamontology.org/data_1566
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Protein structure image
        uri: http://edamontology.org/data_2992
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Chemical structure image
        uri: http://edamontology.org/data_1712
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/poseedit.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T08:58:40.277524Z'
  license: Other
  link:
  - note: A web service to run PoseEdit calculations for protein-ligand complexes.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run PoseEdit calculations for protein-ligand complexes.
    type:
    - Service
    url: https://proteins.plus/help/poseview2_rest
  maturity: Mature
  name: PoseEdit
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1007/s10822-023-00522-4
    metadata: null
    note: null
    pmcid: PMC10440272
    pmid: '37515714'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: geomine
    type: usedBy
  - biotoolsID: protoss
    type: uses
  toolType:
  - Web service
  - Web API
  topic:
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  validated: 0
  version: []
- accessibility: null
  additionDate: '2016-11-21T10:33:07Z'
  biotoolsCURIE: biotools:poseview
  biotoolsID: poseview
  collectionID:
  - de.NBI-biodata
  - de.NBI
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: null
    typeRole:
    - Provider
    url: null
  description: PoseView automatically generates 2D diagrams of protein-ligand complexes,
    focusing on the interactions between protein and ligand. Interactions between
    molecules are estimated by an underlying interaction mode that relies on atom
    types and simple geometric criteria. It adheres to the conventions of chemical
    structure diagram generation. The quality of the resulting diagrams is comparable
    to manually drawn examples from books and scientific publications.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download: []
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: 2D interaction diagram drawing
    operation:
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Residue interaction calculation
      uri: http://edamontology.org/operation_0248
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    - term: Salt bridge calculation
      uri: http://edamontology.org/operation_1839
    - term: Protein-metal contact calculation
      uri: http://edamontology.org/operation_1834
    output:
    - data:
        term: Protein-ligand interaction report
        uri: http://edamontology.org/data_1566
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Chemical structure image
        uri: http://edamontology.org/data_1712
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Protein structure image
        uri: http://edamontology.org/data_2992
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: SVG
        uri: http://edamontology.org/format_3604
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/poseview.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T08:57:26.150042Z'
  license: Other
  link:
  - note: A web service to run PoseView calculations for protein-ligand complexes.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run PoseView calculations for protein-ligand complexes.
    type:
    - Service
    url: https://proteins.plus/help/poseview_rest
  maturity: Mature
  name: PoseView
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1021/ml100164p
    metadata: null
    note: null
    pmcid: PMC4007829
    pmid: '24900245'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btl150
    metadata: null
    note: null
    pmcid: null
    pmid: '16632493'
    type:
    - Benchmarking study
    version: null
  - doi: 10.1002/cmdc.200700010
    metadata: null
    note: null
    pmcid: null
    pmid: '17436259'
    type:
    - Benchmarking study
    version: null
  - doi: 10.1021/ci049958u
    metadata: null
    note: null
    pmcid: null
    pmid: '15154775'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Web API
  - Web service
  topic:
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-11-28T10:07:16Z'
  biotoolsCURIE: biotools:protoss
  biotoolsID: protoss
  collectionID:
  - de.NBI-biodata
  - de.NBI
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: Protoss is a fully automated hydrogen atom placement tool for protein-ligand
    complexes. It adds missing hydrogen atoms to protein structures and detects reasonable
    protonation states, tautomeric states, and hydrogen coordinates of both protein
    and ligand molecules by optimizing the hydrogen bond network.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download: []
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: prediction of protonation states and tautomers and placement of hydrogen
      atoms
    operation:
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/protoss.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T08:56:32.130763Z'
  license: Other
  link:
  - note: A web service to run Protoss calculations.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run Protoss calculations.
    type:
    - Service
    url: https://proteins.plus/help/protoss_rest
  maturity: Mature
  name: Protoss
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1186/1758-2946-6-12
    metadata: null
    note: null
    pmcid: PMC4019353
    pmid: '24694216'
    type:
    - Primary
    version: null
  - doi: 10.1186/1758-2946-1-13
    metadata: null
    note: null
    pmcid: PMC3225823
    pmid: '20298519'
    type:
    - Other
    version: null
  relation:
  - biotoolsID: geomine
    type: usedBy
  - biotoolsID: jamda
    type: usedBy
  toolType:
  - Web API
  - Web service
  topic:
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Structural biology
    uri: http://edamontology.org/topic_1317
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-11-21T10:33:07Z'
  biotoolsCURIE: biotools:dogsitescorer
  biotoolsID: dogsitescorer
  collectionID:
  - de.NBI-biodata
  - de.NBI
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: DoGSiteScorer is a grid-based automated pocket detection and analysis
    tool. It applies a Difference of Gaussian filter to detect potential binding pockets
    and splits them into sub-pockets. The method solely uses the 3D structure of the
    protein. Global properties, describing the size, shape, and chemical features
    of the predicted (sub-)pockets, are calculated. Per default, a simple druggability
    score based on a linear combination of the three descriptors describing volume,
    hydrophobicity, and enclosure is provided for each (sub-)pocket. Furthermore,
    a subset of meaningful descriptors is incorporated in a support vector machine
    (libsvm) to predict the (sub-)pocket druggability score (values are between zero
    and one). The higher the score, the more druggable the pocket is estimated to
    be.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download: []
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: small molecule binding site detection and druggability assessment
    operation:
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    - term: Ligand-binding site prediction
      uri: http://edamontology.org/operation_3897
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
    - data:
        term: Map data
        uri: http://edamontology.org/data_2019
      format: []
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsitescorer.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T08:54:52.480543Z'
  license: Other
  link:
  - note: A web service to run DoGSiteScorer calculations for protein structures stored
      in the Protein Data Bank and AlphaFold Protein Structure Database.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run DoGSiteScorer calculations for protein structures stored
      in the Protein Data Bank and AlphaFold Protein Structure Database.
    type:
    - Service
    url: https://proteins.plus/help/dogsite_rest
  maturity: Mature
  name: DoGSiteScorer
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1021/ci100241y
    metadata: null
    note: null
    pmcid: null
    pmid: '20945875'
    type:
    - Method
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/bts310
    metadata: null
    note: null
    pmcid: null
    pmid: '22628523'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Web API
  - Web service
  topic:
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  validated: 1
  version: []
- accessibility: null
  additionDate: '2025-12-15T10:10:43.359638Z'
  biotoolsCURIE: biotools:dogsite3
  biotoolsID: dogsite3
  collectionID:
  - de.NBI-biodata
  - de.NBI
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
    gridid: null
    name: NAOMI ChemBio Suite Support
    note: Primary Contact for Standalone Tool Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: DoGSite3 was developed for predicting robust and reliable small molecule
    binding sites and computing their geometrical and chemical descriptors. It is
    based on the grid-based DoGSite algorithm for predicting pockets and their sub-pockets.
    The new tool is largely rotation- and translation-invariant due to a normalization
    procedure before binding site prediction. Known ligands in the structure can be
    used to bias the grid by sufficiently buried ligand fragments. The output encompasses
    novel chemical binding site descriptors considering solvent accessibility. Compared
    to its predecessor, it shows increased robustness through comprehensive parameter
    optimization. DoGSite3 runs finish within seconds.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download:
  - note: Please register to download the tool.
    type: Binaries
    url: https://uhh.de/naomi
    version: null
  editPermission:
    authors:
    - ehrt
    - MelanieZBH
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: UniProt accession
        uri: http://edamontology.org/data_3021
      format: []
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: small molecule binding site detection
    operation:
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    - term: Ligand-binding site prediction
      uri: http://edamontology.org/operation_3897
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Map data
        uri: http://edamontology.org/data_2019
      format: []
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsite3.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-12T08:53:05.223278Z'
  license: Other
  link:
  - note: A web service to run DoGSite3 calculations for protein structures stored
      in the Protein Data Bank and AlphaFold Protein Structure Database.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run DoGSite3 calculations for protein structures stored in
      the Protein Data Bank and AlphaFold Protein Structure Database.
    type:
    - Service
    url: https://proteins.plus/help/dogsite3_rest
  - note: Link to download the standalone tool from the NAOMI ChemBio Suite.
    type:
    - Software catalogue
    url: https://uhh.de/naomi
  maturity: Mature
  name: DoGSite3
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1021/acs.jcim.3c00336
    metadata: null
    note: null
    pmcid: null
    pmid: '37130052'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: geomine
    type: usedBy
  toolType:
  - Command-line tool
  - Web API
  - Web service
  topic:
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-08-03T18:52:54Z'
  biotoolsCURIE: biotools:obitools
  biotoolsID: obitools
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: eric.coissac@inria.fr
    fundrefid: null
    gridid: null
    name: Eric Coissac
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://metabarcoding.org/obitools
  description: Set of python programs developed to simplify the manipulation of sequence
    files. They were mainly designed to help us for analyzing Next Generation Sequencer
    outputs (454 or Illumina) in the context of DNA Metabarcoding.
  documentation:
  - note: null
    type:
    - General
    url: http://metabarcoding.org//obitools/doc/welcome.html#installing-the-obitools
  download: []
  editPermission:
    authors:
    - kevin9
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output: []
  homepage: https://git.metabarcoding.org/obitools/obitools/wikis/home
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-12T06:58:21.546910Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/obitools-scripts-and-library-for-sequence-analysis.html
  maturity: null
  name: OBITools
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: mbs_import
  publication:
  - doi: 10.1111/1755-0998.12428
    metadata: null
    note: null
    pmcid: null
    pmid: '25959493'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-03-24T09:56:23Z'
  biotoolsCURIE: biotools:predictprotein
  biotoolsID: predictprotein
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: help@predictprotein.org
    fundrefid: null
    gridid: null
    name: PredictProtein Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: PredictProtein is a protein sequence analysis and structure prediction
    tool.  Users provide a protein sequence, and PredictProtein reports similar sequences,
    PROSITE sequence motifs, and various types of structure prediction information.  You
    can also use META PredictProtein to submit a sequence to one web form and query
    several other servers at once, retrieving the results by e-mail.
  documentation:
  - note: null
    type:
    - General
    url: https://open.predictprotein.org/tutorials
  download: []
  editPermission:
    authors:
    - AIT-IDIR
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Protein secondary structure prediction (helices)
      uri: http://edamontology.org/operation_0468
    - term: Protein fold recognition
      uri: http://edamontology.org/operation_0303
    - term: Protein secondary structure prediction
      uri: http://edamontology.org/operation_0267
    - term: Protein structure prediction
      uri: http://edamontology.org/operation_0474
    output: []
  homepage: http://ppopen.rostlab.org
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-11T10:22:28.635847Z'
  license: null
  link: []
  maturity: null
  name: PredictProtein
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/nar/gkg572
    metadata: null
    note: null
    pmcid: PMC168978
    pmid: '12824314'
    type: []
    version: null
  - doi: 10.1093/nar/gkh377
    metadata: null
    note: null
    pmcid: PMC441515
    pmid: '15215403'
    type: []
    version: null
  - doi: 10.1093/nar/gkg508
    metadata: null
    note: null
    pmcid: PMC168915
    pmid: '12824312'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Protein structural motifs and surfaces
    uri: http://edamontology.org/topic_0166
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-08-03T18:59:55Z'
  biotoolsCURIE: biotools:snap
  biotoolsID: snap
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: ifkorf@ucdavis.edu
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://korflab.ucdavis.edu/
  description: The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.
  documentation:
  - note: null
    type:
    - General
    url: https://korflab.ucdavis.edu/software.html
  download: []
  editPermission:
    authors:
    - ELIXIR-CZ
    - AIT-IDIR
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene prediction
      uri: http://edamontology.org/operation_2454
    output: []
  homepage: https://korflab.ucdavis.edu/software.html
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-06-11T10:22:27.776623Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: https://www.mybiosoftware.com/snap-20130216-gene-prediction-tool.html
  maturity: null
  name: SNAP
  operatingSystem:
  - Linux
  otherID: []
  owner: mbs_import
  publication:
  - doi: 10.1186/1471-2105-5-59
    metadata:
      abstract: Background. Computational gene prediction continues to be an important
        problem, especially for genomes with little experimental data. Results. I
        introduce the SNAP gene finder which has been designed to be easily adaptable
        to a variety of genomes. In novel genomes without an appropriate gene finder,
        I demonstrate that employing a foreign gene finder can produce highly inaccurate
        results, and that the most compatible parameters may not come from the nearest
        phylogenetic neighbor. I find that foreign gene finders are more usefully
        employed to bootstrap parameter estimation and that the resulting parameters
        can be highly accurate. Conclusion.Since gene prediction is sensitive to species-specific
        parameters, every genome needs dedicated gene finder. © 2004 Korf, licensee
        BioMed Central Ltd.
      authors:
      - name: Korf I.
      citationCount: 2108
      date: '2004-05-14T00:00:00Z'
      journal: BMC Bioinformatics
      title: Gene finding in novel genomes
    note: null
    pmcid: PMC421630
    pmid: '15144565'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Genetics
    uri: http://edamontology.org/topic_3053
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2026-06-10T15:44:24.553891Z'
  biotoolsCURIE: biotools:flavotyper
  biotoolsID: flavotyper
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: FlavoTyper is a bioinformatics tool that performs in silico serotyping
    of Flavobacterium psychrophilum genome assemblies.
  documentation:
  - note: null
    type:
    - User manual
    url: https://flavotyper-125bcf.pages-forge.inrae.fr/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    output: []
  homepage: https://forge.inrae.fr/eric.duchaud/flavotyper
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-10T17:14:53.654094Z'
  license: Apache-2.0
  link: []
  maturity: Emerging
  name: FlavoTyper
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Salmam2
  publication: []
  relation: []
  toolType:
  - Command-line tool
  - Web service
  topic:
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Veterinary medicine
    uri: http://edamontology.org/topic_3397
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-06-10T14:01:27.924178Z'
  biotoolsCURIE: biotools:monai_label
  biotoolsID: monai_label
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: MONAI Label is an intelligent open source image labeling and learning
    tool that enables users to create annotated datasets and build AI annotation models
    for clinical evaluation. MONAI Label enables application developers to build labeling
    apps in a serverless way, where custom labeling apps are exposed as a service
    through the MONAI Label Server.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output: []
  homepage: https://monai.readthedocs.io/projects/label/en/latest/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-10T14:01:27.926674Z'
  license: Apache-2.0
  link: []
  maturity: Mature
  name: MONAI Label
  operatingSystem:
  - Linux
  - Windows
  otherID: []
  owner: walter3
  publication:
  - doi: 10.1007/978-3-031-17027-0_2
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Medicine
    uri: http://edamontology.org/topic_3303
  validated: 0
  version:
  - 0.8.5
- accessibility: null
  additionDate: '2026-06-10T13:16:41.434931Z'
  biotoolsCURIE: biotools:deepconsensus
  biotoolsID: deepconsensus
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: DeepConsensus uses gap-aware sequence transformers to correct errors
    in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: deepconsensus run --subreads_to_ccs=shard_id.subreads_to_ccs.bam  --ccs_bam=shard_id.ccs.bam
      --checkpoint=model/checkpoint --output=shard_id.output.fastq
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format: []
  homepage: https://github.com/google/deepconsensus
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-10T13:16:41.436989Z'
  license: BSD-3-Clause
  link: []
  maturity: Mature
  name: DeepConsensus
  operatingSystem:
  - Linux
  otherID: []
  owner: walter3
  publication:
  - doi: 10.1038/s41587-022-01435-7
    metadata: null
    note: null
    pmcid: null
    pmid: '36050551'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  validated: 0
  version:
  - 1.2.0
- accessibility: null
  additionDate: '2026-06-10T12:31:35.126196Z'
  biotoolsCURIE: biotools:dazz_db
  biotoolsID: dazz_db
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A database system designed to store, organize, and manage large-scale
    nucleotide sequencing read data (like PacBio reads) for the Dazzler genome assembler
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 1. fasta2DB [-v] <path:db> ( -f<file> | -i[<name>] | <input:fasta> ... )
    input:
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format: []
    note: null
    operation:
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    output:
    - data:
        term: Data reference
        uri: http://edamontology.org/data_2093
      format: []
  homepage: https://github.com/thegenemyers/DAZZ_DB
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-06-10T12:31:35.128776Z'
  license: Other
  link: []
  maturity: Legacy
  name: DAZZ_DB
  operatingSystem:
  - Linux
  otherID: []
  owner: walter3
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2026-06-09T14:59:46.648310Z'
  biotoolsCURIE: biotools:sigmacv
  biotoolsID: sigmacv
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: chretien.basile.jean.bernard.u4@s.mail.nagoya-u.ac.jp
    fundrefid: null
    gridid: null
    name: Basile Chrétien
    note: null
    orcidid: https://orcid.org/0000-0002-7483-2489
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    - Maintainer
    - Primary contact
    url: null
  description: Auto-generates clean, customizable academic CVs from open research
    data (OpenAlex, ORCID, Crossref, DataCite, Open Editors Plus). A single canonical
    CV object drives every output format (HTML, PDF, DOCX, LaTeX, Markdown); citations
    render through CSL; and the account holder is matched by persistent identifier
    (ORCID / OpenAlex ID) rather than name string. Free for individuals, open-source,
    and FAIR by design.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/BasileChretien/sigmacv#readme
  download:
  - note: null
    type: Source code
    url: https://github.com/BasileChretien/sigmacv
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data formatting
      uri: http://edamontology.org/operation_0335
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    output: []
  homepage: https://sigmacv.org
  homepage_status: 0
  language:
  - JavaScript
  - TypeScript
  lastUpdate: '2026-06-09T14:59:46.652232Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/BasileChretien/sigmacv
  - note: null
    type:
    - Issue tracker
    url: https://github.com/BasileChretien/sigmacv/issues
  maturity: Mature
  name: SigmaCV
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: basile
  publication:
  - doi: 10.5281/zenodo.20594123
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: 0.1.0
  relation: []
  toolType:
  - Web application
  topic: []
  validated: 0
  version:
  - 0.1.0
- accessibility: Open access
  additionDate: '2015-10-07T18:29:49Z'
  biotoolsCURIE: biotools:pdb-redo
  biotoolsID: pdb-redo
  collectionID:
  - 3D-BioInfo
  - 3D-BioInfo-Nucleic-Acid
  - DRCAT
  - 3D-BioInfo-Protein-Ligand-Interactions
  - INSTRUCT
  - 3D-BioInfo-Structure-Function
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: r.joosten@nki.nl
    fundrefid: null
    gridid: null
    name: Robbie P. Joosten
    note: null
    orcidid: https://orcid.org/0000-0002-2323-2686
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: null
  - email: vriend@cmbi.ru.nl
    fundrefid: null
    gridid: null
    name: Gert Vriend
    note: Project initiator
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: a.perrakis@nki.nl
    fundrefid: null
    gridid: null
    name: Anastassis Perrakis
    note: null
    orcidid: https://orcid.org/0000-0002-1151-6227
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: m.hekkelman@nki.nl
    fundrefid: null
    gridid: null
    name: Maarten Hekkelman
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Bart van Beusekom
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Krista Joosten
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Netherlands Organization for Scientific Research (NWO)
    note: Various grants (Veni, Vidi, TOP)
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: West-Life Horizon 2020
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: iNEXT
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Wouter Touw
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: The Netherlands Cancer Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: CCP4
    note: Financial and other support
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Contributor
    url: https://www.ccp4.ac.uk
  description: Databank of optimised macromolecular structures. PDB-REDO entries are
    refined, rebuilt and validated with one consistent protocol using the equivalent
    entry in the Protein Data Bank and its experimental data. PDB-REDO entries typically
    have higher structural quality and a better fit to the experimental data.
  documentation:
  - note: null
    type:
    - General
    url: https://pdb-redo.eu
  download:
  - note: null
    type: Downloads page
    url: https://pdb-redo.eu/download-info.html
    version: null
  editPermission:
    authors:
    - rjoosten
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode: []
  elixirPlatform:
  - Data
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: PDB ID
        uri: http://edamontology.org/data_1127
      format: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: Structure
        uri: http://edamontology.org/data_0883
      format:
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein structural quality report
        uri: http://edamontology.org/data_1539
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Electron density map
        uri: http://edamontology.org/data_0937
      format: []
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: dssp
        uri: http://edamontology.org/format_1454
  homepage: https://pdb-redo.eu
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-09T13:12:57.194510Z'
  license: Freeware
  link:
  - note: Repository for main software pipeline
    type:
    - Repository
    url: https://github.com/PDB-REDO/pdb-redo-main
  - note: Library code for pdb-redo tools
    type:
    - Repository
    url: https://github.com/PDB-REDO/libpdb-redo
  - note: Repository for the web interface including the API
    type:
    - Repository
    url: https://github.com/PDB-REDO/pdb-redo-session-manager
  maturity: Mature
  name: PDB-REDO databank of optimised macromolecular structures
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: rjoosten
  publication:
  - doi: 10.1107/s0907444911054515
    metadata: null
    note: null
    pmcid: PMC3322608
    pmid: '22505269'
    type: []
    version: null
  - doi: 10.1107/s0021889809008784
    metadata: null
    note: null
    pmcid: PMC3246819
    pmid: '22477769'
    type: []
    version: null
  - doi: 10.1107/s0907444908037591
    metadata: null
    note: null
    pmcid: PMC2631631
    pmid: '19171973'
    type: []
    version: null
  - doi: 10.1107/s2052252518010552
    metadata: null
    note: null
    pmcid: PMC6126648
    pmid: '30224962'
    type: []
    version: null
  - doi: 10.1002/pro.3353
    metadata: null
    note: Algorithms for homology restrains; new databank
    pmcid: PMC5818736
    pmid: '29168245'
    type:
    - Method
    version: '7'
  - doi: 10.1093/bioinformatics/btr590
    metadata: null
    note: Algorithms for model rebuilding
    pmcid: PMC3232375
    pmid: '22034521'
    type:
    - Method
    version: null
  - doi: 10.1016/j.jmb.2016.02.002
    metadata: null
    note: Algorithms for correction and completion of N-glycosylation sites
    pmcid: null
    pmid: '26869101'
    type:
    - Method
    version: null
  - doi: 10.1107/s2059798316013036
    metadata: null
    note: null
    pmcid: PMC5053137
    pmid: '27710932'
    type: []
    version: null
  - doi: 10.1107/s2059798319003875
    metadata: null
    note: null
    pmcid: PMC6465985
    pmid: '30988258'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-08-13T19:15:03Z'
  biotoolsCURIE: biotools:grnsight
  biotoolsID: grnsight
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Alex Miller
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jia Celyne Garcia
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Cindy Tong
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Amelie Dinh
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Milka Zekarias
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ngoc Kim Ngan Tran
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Cecilia Zaragoza
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: A’Kaia Phelps
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ona O. Igbinedion
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ahmad R. Mersaghian
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ian M. Green
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Lauren L. Amparo
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Alexia M. Filler
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kevin B. Patterson
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: John L. Lopez
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Justin Kyle T. Torres
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Eileen Choe
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jen Shin
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Mihir Samdarshi
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Anindita Varshneya
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nicole A. Anguiano
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Britain J. Southwick
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ben G. Fitzpatrick
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Loyola Marymount University
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: NSF award 0921038; LMU Rains Research Assistant Program; LMU Summer Undergraduate
      Research Program
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: lmu.edu
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: kdahlquist@lmu.edu
    fundrefid: null
    gridid: null
    name: Kam D. Dahlquist
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: dondi@lmu.edu
    fundrefid: null
    gridid: null
    name: John David N. Dionisio
    note: null
    orcidid: https://orcid.org/0000-0001-8655-4693
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Web application and service for visualizing small- to medium-scale
    models of gene regulatory networks. It automatically lays out either an unweighted
    or weighted network graph based on an Excel input spreadsheet containing an adjacency
    matrix where regulators are named in the columns and target genes in the rows.
    It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges
    and has general applicability.
  documentation:
  - note: null
    type:
    - General
    url: http://dondi.github.io/GRNsight/documentation.html
  download:
  - note: null
    type: Source code
    url: https://github.com/dondi/GRNsight/archive/refs/heads/main.zip
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: GRNsight automatically lays out a network graph based on an Excel input
      spreadsheet containing an adjacency matrix where regulators are named in the
      columns and target genes in the rows. When a user uploads a spreadsheet with
      an unweighted adjacency matrix, GRNsight automatically lays out the graph using
      black lines and pointed arrowheads.  When a user uploads a spreadsheet with
      a weighted adjacency matrix, GRNsight uses pointed and blunt arrowheads, and
      colors the edges and adjusts their thicknesses based on the sign (positive for
      activation or negative for repression) and magnitude of the weight parameter.
      Nodes are rectangular and support gene labels of up to 12 characters.  The edges
      are arcs, which become straight lines when the nodes are close together.  Self-regulatory
      edges are indicated by a loop on the lower-right side of a node. Visualizations
      can be modified by sliders that adjust D3.js's force graph layout parameters
      and through manual node dragging.
    operation:
    - term: Gene regulatory network analysis
      uri: http://edamontology.org/operation_1781
    - term: Pathway or network visualisation
      uri: http://edamontology.org/operation_3083
    output: []
  homepage: http://dondi.github.io/GRNsight/
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2026-06-07T23:16:02.636376Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/dondi/GRNsight
  maturity: Mature
  name: GRNsight
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: dondi@lmu.edu
  publication:
  - doi: 10.7717/peerj-cs.85
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.5281/zenodo.7411630
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  validated: 1
  version:
  - 7.8.0
- accessibility: null
  additionDate: '2026-06-06T13:23:36.312620Z'
  biotoolsCURIE: biotools:mol_biology_tools
  biotoolsID: mol_biology_tools
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: rpjscience@gmail.com
    fundrefid: null
    gridid: null
    name: Dr. Rohit P James
    note: Dr. Rohit P James graduated from IIT Bombay. He works on biocatalysis and
      enzyme engineering.
    orcidid: https://orcid.org/0009-0003-9347-2014
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    - Provider
    url: null
  description: Mol Biology Tools is a free browser-based collection of molecular biology
    utilities for routine sequence analysis, primer design, Sanger sequencing primer
    planning, cloning setup, and wet-lab calculations. The site includes tools for
    PCR primer design, Sanger primer design and primer walking, primer binding checks,
    restriction site analysis, reverse complement generation, ORF and protein translation,
    codon optimization, ligation calculations, molarity calculations, dilution calculations,
    and multi-solute solution recipe preparation. The tools run in the browser and
    are intended for quick experimental planning without requiring logins or server-side
    sequence upload.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://molbiologytools.com/help_guides
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: PCR primer design
      uri: http://edamontology.org/operation_0308
    output: []
  homepage: https://molbiologytools.com/
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2026-06-06T13:36:20.538884Z'
  license: Proprietary
  link:
  - note: Landing page with all tools listed.
    type:
    - Software catalogue
    - Repository
    url: https://molbiologytools.com/
  - note: Searchable FAQ covering primer design, Sanger sequencing, restriction sites,
      sequence checks, molarity, dilution, ligation, and connected tool workflows.
    type:
    - Other
    url: https://molbiologytools.com/faq
  - note: PCR primer design tool for raw DNA, FASTA, or GenBank templates, with primer
      length or target Tm modes and optional restriction-enzyme overhang planning.
    type:
    - Service
    url: https://molbiologytools.com/primer_design
  - note: Primer binding checker for linear or circular DNA templates, including binding
      positions, amplicon size, strand direction, and product checks.
    type:
    - Service
    url: https://molbiologytools.com/primer_binding_checker
  - note: Restriction enzyme site analyzer for linear or circular DNA, FASTA, or GenBank
      input, with enzyme cut-site detection and sequence-to-primer workflow links.
    type:
    - Service
    url: https://molbiologytools.com/restriction_site_analyzer
  - note: Molarity calculator and multi-solute recipe builder for lab solutions, molecular
      weight, percent w/v, compound search, 1X recipes, and stock-multiplier outputs.
    type:
    - Service
    url: https://molbiologytools.com/molarity_calculator
  - note: DNA ligation calculator for cloning setup, vector mass, insert length, insert-to-vector
      molar ratio, and insert mass calculation.
    type:
    - Service
    url: https://molbiologytools.com/ligation_calculator
  maturity: Emerging
  name: Mol Biology Tools
  operatingSystem:
  - Windows
  - Mac
  - iOS
  - Linux
  - Android
  otherID: []
  owner: rohit1
  publication: []
  relation: []
  toolType:
  - Web service
  topic:
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  - term: Biotechnology
    uri: http://edamontology.org/topic_3297
  - term: Synthetic biology
    uri: http://edamontology.org/topic_3895
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-12-18T00:03:45Z'
  biotoolsCURIE: biotools:autodock_vina
  biotoolsID: autodock_vina
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://olegtrott.com/
  description: AutoDock Vina is a new open-source program for drug discovery, molecular
    docking and virtual screening, offering multi-core capability, high performance
    and enhanced accuracy and ease of use.
  documentation:
  - note: null
    type:
    - User manual
    url: http://vina.scripps.edu/manual.html
  download: []
  editPermission:
    authors:
    - ragibsiddique
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Molecular docking
      uri: http://edamontology.org/operation_0478
    output: []
  homepage: http://vina.scripps.edu/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-06-04T08:07:30.690513Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/autodock-vina-1-1-2-molecular-docking-virtual-screening-program.html
  maturity: null
  name: AutoDock Vina
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID:
  - type: rrid
    value: RRID:SCR_011958
    version: null
  owner: monami
  publication:
  - doi: 10.1002/jcc.21334
    metadata: null
    note: null
    pmcid: PMC3041641
    pmid: '19499576'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Molecular docking
    uri: http://edamontology.org/topic_2275
  validated: 1
  version:
  - 1.1.2
- accessibility: null
  additionDate: '2017-08-03T18:57:46Z'
  biotoolsCURIE: biotools:rexprimer
  biotoolsID: rexprimer
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: chumpol.nga@biotec.or.th
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www4a.biotec.or.th/GI
  description: A web application that provides many functionalities for improved PCR
    primer design.
  documentation:
  - note: null
    type:
    - User manual
    url: http://www4a.biotec.or.th/rexprimer/help/User_Manual.html
  download: []
  editPermission:
    authors:
    - Listi
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: PCR primer design
      uri: http://edamontology.org/operation_0308
    output: []
  homepage: http://www4a.biotec.or.th/rexprimer/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-04T08:07:29.277429Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/rexprimer-web-based-application-for-primer-design.html
  maturity: null
  name: RExPrimer
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: mbs_import
  publication:
  - doi: 10.1186/1471-2164-10-s3-s4
    metadata: null
    note: null
    pmcid: PMC2788391
    pmid: '19958502'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Nucleic acid sites, features and motifs
    uri: http://edamontology.org/topic_3511
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Probes and primers
    uri: http://edamontology.org/topic_0632
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2015-06-11T13:36:28Z'
  biotoolsCURIE: biotools:ega
  biotoolsID: ega
  collectionID:
  - RD-connect
  - Rare Disease
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: EMBL-EBI Databases
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: helpdesk@ega-archive.org
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: European genome-phenome Archive (EGA) - service for permanent archiving
    and sharing of all types of personally identifiable genetic and phenotypic data
    resulting from biomedical research projects.
  documentation:
  - note: null
    type:
    - General
    url: https://ega-archive.org/
  download: []
  editPermission:
    authors:
    - ELIXIR-EE
    - amy_jean
    type: group
  elixirCommunity: []
  elixirNode:
  - Spain
  elixirPlatform:
  - Data
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: EGA accession
        uri: http://edamontology.org/data_2383
      format: []
    note: null
    operation:
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    output:
    - data:
        term: Experiment report
        uri: http://edamontology.org/data_2531
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://ega-archive.org/
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2026-06-04T08:07:27.522383Z'
  license: null
  link: []
  maturity: Mature
  name: EGA
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: EMBL-EBI_Databases
  publication:
  - doi: 10.1038/ng.3312
    metadata:
      abstract: © 2015 Nature America, Inc. All rights reserved.The European Genome-phenome
        Archive (EGA) is a permanent archive that promotes the distribution and sharing
        of genetic and phenotypic data consented for specific approved uses but not
        fully open, public distribution. The EGA follows strict protocols for information
        management, data storage, security and dissemination. Authorized access to
        the data is managed in partnership with the data-providing organizations.
        The EGA includes major reference data collections for human genetics research.
      authors:
      - name: Lappalainen I.
      - name: Almeida-King J.
      - name: Kumanduri V.
      - name: Senf A.
      - name: Spalding J.D.
      - name: Ur-Rehman S.
      - name: Saunders G.
      - name: Kandasamy J.
      - name: Caccamo M.
      - name: Leinonen R.
      - name: Vaughan B.
      - name: Laurent T.
      - name: Rowland F.
      - name: Marin-Garcia P.
      - name: Barker J.
      - name: Jokinen P.
      - name: Torres A.C.
      - name: De Argila J.R.
      - name: Llobet O.M.
      - name: Medina I.
      - name: Puy M.S.
      - name: Alberich M.
      - name: De La Torre S.
      - name: Navarro A.
      - name: Paschall J.
      - name: Flicek P.
      citationCount: 161
      date: '2015-01-01T00:00:00Z'
      journal: Nature Genetics
      title: The European Genome-phenome Archive of human data consented for biomedical
        research
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web API
  - Web application
  - Database portal
  topic:
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Laboratory information management
    uri: http://edamontology.org/topic_0607
  - term: Data security
    uri: http://edamontology.org/topic_3263
  - term: Data integration and warehousing
    uri: http://edamontology.org/topic_3366
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-05-16T13:43:29Z'
  biotoolsCURIE: biotools:phylip
  biotoolsID: phylip
  collectionID:
  - Animal and Crop Genomics
  confidence_flag: null
  cost: null
  credit:
  - email: joe@gs.washington.edu
    fundrefid: null
    gridid: null
    name: Joe Felsenstein
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://evolution.gs.washington.edu/felsenstein.html
  description: Comprehensive set of programs for phylogenetic analyses; available
    for PC and Mac; source code available for easy compiling in UNIX.
  documentation:
  - note: null
    type:
    - General
    url: http://evolution.genetics.washington.edu/phylip/phylip.html
  download: []
  editPermission:
    authors:
    - animalandcropgenomics
    - Emra
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Phylogenetic tree bootstrapping
      uri: http://edamontology.org/operation_0552
    - term: Phylogenetic tree distances calculation
      uri: http://edamontology.org/operation_0557
    - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods)
      uri: http://edamontology.org/operation_0547
    - term: Phylogenetic tree generation (parsimony methods)
      uri: http://edamontology.org/operation_0545
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    output: []
  homepage: http://evolution.genetics.washington.edu/phylip.html
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-06-04T08:07:26.784924Z'
  license: BSD-3-Clause
  link: []
  maturity: null
  name: PHYLIP
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID:
  - type: rrid
    value: 'RRID: SCR_006244'
    version: null
  owner: ELIXIR-EE
  publication:
  - doi: 10.1371/journal.pone.0013999
    metadata:
      abstract: 'Background: Phylogenetic study of protein sequences provides unique
        and valuable insights into the molecular and genetic basis of important medical
        and epidemiological problems as well as insights about the origins and development
        of physiological features in present day organisms. Consensus phylogenies
        based on the bootstrap and other resampling methods play a crucial part in
        analyzing the robustness of the trees produced for these analyses. Methodology:
        Our focus was to increase the number of bootstrap replications that can be
        performed on large protein datasets using the maximum parsimony, distance
        matrix, and maximum likelihood methods. We have modified the PHYLIP package
        using MPI to enable large-scale phylogenetic study of protein sequences, using
        a statistically robust number of bootstrapped datasets, to be performed in
        a moderate amount of time. This paper discusses the methodology used to parallelize
        the PHYLIP programs and reports the performance of the parallel PHYLIP programs
        that are relevant to the study of protein evolution on several protein datasets.
        Conclusions: Calculations that currently take a few days on a state of the
        art desktop workstation are reduced to calculations that can be performed
        over lunchtime on a modern parallel computer. Of the three protein methods
        tested, the maximum likelihood method scales the best, followed by the distance
        method, and then the maximum parsimony method. However, the maximum likelihood
        method requires significant memory resources, which limits its application
        to more moderately sized protein datasets. © 2010 Ropelewski et al.'
      authors:
      - name: Ropelewski A.J.
      - name: Nicholas H.B.
      - name: Mendez R.R.G.
      citationCount: 13
      date: '2010-12-09T00:00:00Z'
      journal: PLoS ONE
      title: 'MPI-PHYLIP: Parallelizing computationally intensive phylogenetic analysis
        routines for the analysis of large protein families'
    note: null
    pmcid: PMC2981553
    pmid: '21085574'
    type: []
    version: null
  - doi: 10.1385/1-59259-192-2:243
    metadata: null
    note: null
    pmcid: null
    pmid: '10547839'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Physiology
    uri: http://edamontology.org/topic_3300
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2020-06-05T08:52:25Z'
  biotoolsCURIE: biotools:calibracurve
  biotoolsID: calibracurve
  collectionID:
  - BioInfra.Prot
  - de.NBI
  - CUBiMed.RUB
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: martin.eisenacher@rub.de
    fundrefid: null
    gridid: null
    name: PD Dr. Martin Eisenacher
    note: If contacting use "SPARROW" in subject line to avoid mail deluge.
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: de.NBI
    note: Service provision and maintenance funded by de.NBI.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    - Maintainer
    - Support
    url: https://www.denbi.de/
  - email: michael.kohl@rub.de
    fundrefid: null
    gridid: null
    name: Dr. Michael Kohl
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: A highly useful and flexible tool for calibration of targeted MS‐based
    measurements. CalibraCurve enables an automated batch-mode determination of dynamic
    linear ranges and quantification limits for both targeted proteomics and similar
    assays. The software uses a variety of measures to assess the accuracy of the
    calibration and provides intuitive visualizations.
  documentation:
  - note: null
    type:
    - Installation instructions
    - Citation instructions
    - General
    - User manual
    - Training material
    - Terms of use
    url: https://github.com/mpc-bioinformatics/CalibraCurve
  download:
  - note: null
    type: Downloads page
    url: https://github.com/mpc-bioinformatics/CalibraCurve
    version: '2.0'
  editPermission:
    authors:
    - karin
    type: group
  elixirCommunity:
  - Proteomics
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Analysis
      uri: http://edamontology.org/operation_2945
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: tiff
        uri: http://edamontology.org/format_3591
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://github.com/mpc-bioinformatics/CalibraCurve
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-06-04T08:07:22.002962Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/mpc-bioinformatics/CalibraCurve
  maturity: Mature
  name: CalibraCurve
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: BioInfra.Prot
  publication:
  - doi: 10.1002/pmic.201900143
    metadata:
      abstract: Targeted proteomics techniques allow accurate quantitative measurements
        of analytes in complex matrices with dynamic linear ranges that span up to
        4–5 orders of magnitude. Hence, targeted methods are promising for the development
        of robust protein assays in several sensitive areas, for example, in health
        care. However, exploiting the full method potential requires reliable determination
        of the dynamic range along with related quantification limits for each analyte.
        Here, a software named CalibraCurve that enables an automated batch-mode determination
        of dynamic linear ranges and quantification limits for both targeted proteomics
        and similar assays is presented. The software uses a variety of measures to
        assess the accuracy of the calibration, namely precision and trueness. Two
        different kinds of customizable graphs are created (calibration curves and
        response factor plots). The accuracy measures and the graphs offer an intuitive,
        detailed, and reliable opportunity to assess the quality of the model fit.
        Thus, CalibraCurve is deemed a highly useful and flexible tool to facilitate
        the development and control of reliable SRM/MRM-MS-based proteomics assays.
      authors:
      - name: Kohl M.
      - name: Stepath M.
      - name: Bracht T.
      - name: Megger D.A.
      - name: Sitek B.
      - name: Marcus K.
      - name: Eisenacher M.
      citationCount: 4
      date: '2020-06-01T00:00:00Z'
      journal: Proteomics
      title: 'CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements'
    note: null
    pmcid: null
    pmid: '32086983'
    type:
    - Primary
    version: '2.0'
  relation: []
  toolType:
  - Workflow
  - Script
  - Desktop application
  - Plug-in
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Experimental design and studies
    uri: http://edamontology.org/topic_3678
  validated: 1
  version:
  - '2.0'
- accessibility: null
  additionDate: '2026-06-04T08:03:00.099669Z'
  biotoolsCURIE: biotools:maeparser
  biotoolsID: maeparser
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: maeparser is a parser for Schrodinger Maestro files.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Structure
        uri: http://edamontology.org/data_0883
      format: []
    note: null
    operation:
    - term: Data parsing
      uri: http://edamontology.org/operation_1812
    output: []
  homepage: https://github.com/schrodinger/maeparser
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-06-04T08:03:00.102041Z'
  license: MIT
  link: []
  maturity: Mature
  name: maeparser
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: veitveit11
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Structural biology
    uri: http://edamontology.org/topic_1317
  validated: 0
  version:
  - v1.3.3
- accessibility: null
  additionDate: '2026-06-04T07:54:19.689100Z'
  biotoolsCURIE: biotools:LongTR
  biotoolsID: LongTR
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Tandem repeat genotyping with long reads, being a modified version
    of HipSTR.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: BED
        uri: http://edamontology.org/format_3003
      - term: BAM
        uri: http://edamontology.org/format_2572
    note: null
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: https://github.com/gymrek-lab/LongTR
  homepage_status: 0
  language:
  - Python
  - C++
  - C
  - Shell
  lastUpdate: '2026-06-04T07:54:19.694217Z'
  license: GPL-2.0
  link: []
  maturity: Mature
  name: LongTR
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: veitveit11
  publication:
  - doi: 10.1186/s13059-024-03319-2
    metadata: null
    note: null
    pmcid: PMC11229021
    pmid: '38965568'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Long-read sequencing
    uri: http://edamontology.org/topic_4056
  validated: 0
  version:
  - v1.2
- accessibility: null
  additionDate: '2026-06-03T05:24:59.073336Z'
  biotoolsCURIE: biotools:influential
  biotoolsID: influential
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: A comprehensive R package for identifying and ranking influential nodes
    in biological and other complex networks. The package implements the Integrated
    Value of Influence (IVI), Experimental data-based Integrative Ranking (ExIR),
    SIRIR, and numerous network centrality measures, enabling network topology analysis,
    influential node detection, feature prioritization, and candidate biomarker discovery.
    It also provides functions for network reconstruction, centrality assessment,
    visualization, and analysis of relationships between centrality measures.
  documentation:
  - note: null
    type:
    - User manual
    url: https://asalavaty.github.io/influential/articles/Vignettes.html
  download:
  - note: null
    type: Downloads page
    url: https://github.com/asalavaty/influential
    version: null
  - note: CRAN Version
    type: Downloads page
    url: https://cran.r-project.org/package=influential
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 'ivi()

      exir()'
    input: []
    note: 'Identification of influential nodes

      Network centrality analysis

      Feature prioritization and ranking

      Network reconstruction

      Biomarker candidate discovery

      Topological network analysis

      Integrative ranking'
    operation:
    - term: Expression analysis
      uri: http://edamontology.org/operation_2495
    - term: Network analysis
      uri: http://edamontology.org/operation_3927
    output: []
  homepage: https://asalavaty.github.io/influential/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-06-03T05:24:59.075786Z'
  license: GPL-3.0
  link:
  - note: Source code
    type:
    - Repository
    url: https://github.com/asalavaty/influential
  - note: Documentation
    type:
    - Other
    url: https://asalavaty.github.io/influential/
  maturity: Mature
  name: influential
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: mania.abbas
  publication:
  - doi: 10.1016/j.patter.2020.100052
    metadata: null
    note: null
    pmcid: PMC7660386
    pmid: '33205118'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-06-03T01:24:52.152590Z'
  biotoolsCURIE: biotools:cellseekr
  biotoolsID: cellseekr
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: contact@cellseekr.com
    fundrefid: null
    gridid: null
    name: Sandro Matosevic
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: CellSeekr is a customizable discovery platform for the exploration
    and identification of immune signatures in a variety of tumors, patient and treatment
    settings through scRNAseq data analysis.
  documentation:
  - note: null
    type:
    - User manual
    url: http://cellseekr.com/documentation
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: RNA-Seq quantification
      uri: http://edamontology.org/operation_3800
    - term: Expression profile clustering
      uri: http://edamontology.org/operation_0313
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: http://cellseekr.com
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-03T01:37:06.670611Z'
  license: null
  link: []
  maturity: null
  name: CellSeekr
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: sandro
  publication: []
  relation: []
  toolType:
  - Web service
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Allergy, clinical immunology and immunotherapeutics
    uri: http://edamontology.org/topic_3400
  - term: Immunology
    uri: http://edamontology.org/topic_0804
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-05-27T22:24:31.685869Z'
  biotoolsCURIE: biotools:pathogensurveillance
  biotoolsID: pathogensurveillance
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Pathogensurveillance is a population genomics pipeline for pathogen
    identification, variant detection, and biosurveillance. The pipeline accepts paths
    to raw reads for one or more organisms and creates reports in the form of an interactive
    HTML document. Significant features include the ability to analyze unidentified
    eukaryotic and prokaryotic samples, creation of reports for multiple user-defined
    groupings of samples, automated discovery and downloading of reference assemblies
    from NCBI RefSeq, and rapid initial identification based on k-mer sketches followed
    by a more robust multi gene phylogeny and SNP-based phylogeny.
  documentation:
  - note: null
    type:
    - User manual
    url: https://nf-co.re/pathogensurveillance
  download:
  - note: null
    type: Source code
    url: https://github.com/nf-core/pathogensurveillance/archive/refs/tags/1.1.0.tar.gz
    version: 1.1.0
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://nf-co.re/pathogensurveillance/
  homepage_status: 0
  language:
  - Groovy
  - R
  - Bash
  lastUpdate: '2026-05-27T22:31:22.963863Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/nf-core/pathogensurveillance
  - note: null
    type:
    - Issue tracker
    url: https://github.com/nf-core/pathogensurveillance/issues
  maturity: Emerging
  name: pathogensurveillance
  operatingSystem:
  - Linux
  otherID: []
  owner: zachary-foster
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T10:41:57.535794Z'
  biotoolsCURIE: biotools:cluster_based_harmonization
  biotoolsID: cluster_based_harmonization
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: aikaterini_vraka@iislafe.es
    fundrefid: null
    gridid: null
    name: Aikaterini Vraka
    note: null
    orcidid: https://orcid.org/0000-0001-5984-904X
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martínez-Gironés
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Support
    url: null
  description: 'The tool is designed to perform radiomics harmonization on large and
    heterogeneous datasets, where the risk of over-harmonization is present. Instead
    of directly applying harmonization based on predefined batch labels, the tool
    first identifies groups of batches that share similar characteristics through
    clustering of the radiomics data. It then performs harmonization using these cluster-derived
    labels. The tool allows the harmonization of radiomics variables using two methods:
    (1) original ComBat (Rabinovic, 2007) method, where each original batch group
    is considered for the harmonization process and (2) cluster-based ComBat method,
    where batch groups with similar radiomics characteristics form clusters and the
    latter are being considered for the harmonization process.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/Kz3jfQYQZjezpxK
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/5bMA2jsZTfS8eoZ
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=0GJqNJv-Qf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=31
  - note: null
    type:
    - General
    url: https://drive.eucaim.cancerimage.eu/s/LkczHCMZH5nd8QR
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run --rm --cpus CPUS -v input_path:/input -v output_path:/output -v
      config_path:/config harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0
      --config /config/config.json
    input:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    output:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: TIDE TXT
        uri: http://edamontology.org/format_3835
  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0
      --file_path /input/data.xlsx --identifier patient_id --start_col original_shape_Elongation
      --end_col lbp-3D-k_ngtdm_Strength --batch_col software_versions --output_dir
      /output/results --min_clusters 2 --max_clusters 100 --results full --approach
      soft --small_groups merge
    input:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    output:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: TIDE TXT
        uri: http://edamontology.org/format_3835
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:21:17.961394Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Emerging
  name: Cluster based harmonization (EUCAIM-SW-044_T-01-03-006)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-06-06T10:00:26.469620Z'
  biotoolsCURIE: biotools:2d_digital_mammography_harmonization
  biotoolsID: 2d_digital_mammography_harmonization
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: manuel_marfil@iislafe.es
    fundrefid: null
    gridid: null
    name: Manuel Marfil-Trujillo
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Support
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  description: This preprocessing tool is design for 2D digital mammograms in DICOM  format.
    It standardizes and harmonizes images through a configurable pipeline that includes
    spatial reorientation, pseudo-3D stacking, isotropic resampling, intensity normalization,
    optional denoising, contrast enhancement, and mask processing (if available).
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/CC3yJTjPz9N7Ggg
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/rdHWqMkNf7frQRY
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=IrZhMp2lB7g&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=13
  download: []
  editPermission:
    authors:
    - casopon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run -it --rm --name container_name -v "<input_path>:/input" -v "<output_path>:/output"
      -v "<config_path>:/config" harbor.eucaim.cancerimage.eu/processing-tools/2d_digital_mammography_harmonization:1.1.0
      /app/entrypoint.sh --config /config/config.json
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/2d_digital_mammography_harmonization:1.1.0
      --input_directory dataset_id --output_directory gaussian_output --num_workers
      4 --series_number 2301101 --series_description_suffix _harmonized --zscore_enabled
      true --zscore_p_low 1.0 --zscore_p_high 99.0 --denoise_method gaussian --gaussian_ksize
      3 --gaussian_sigma 0.8 --clahe_enabled true --clahe_clip_limit 0.01
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Command Arguments
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/2d_digital_mammography_harmonization/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:21:05.356361Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/2d_digital_mammography_harmonization/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Emerging
  name: 2D Digital Mammography Harmonization (EUCAIM-SW-046_T-01-03-008)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T10:38:08.771699Z'
  biotoolsCURIE: biotools:ct-based_neuroblastoma_tumour_detection_and_segmentation
  biotoolsID: ct-based_neuroblastoma_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Support
    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: The tool performs by deep learning an automatic segmentation of the
    possible neuroblastoma tumours on Contrast Enhanced CT images (CE-CTs). Model
    architecture is Unet-based with residual operations, atrous dilation convolution
    and specific batch generator. It applies preprocessing steps as RAS conversion,
    resizing, z-score normalization, patching; and postprocessing operations. It takes
    DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/GxJrJPrYBnzecqT
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=JQ0dtAE_6uc&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=37
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run --rm --gpus all \\\n\t-v /path/to/input:/input \\\n\t-v /path/to/output:/output\
      \ \\\n\tharbor.eucaim.cancerimage.eu/processing-tools/ct-based_neuroblastoma_tumour_detection_and_segmentation:2.0.0\
      \ \\\n\t--series_csv /output/config/series_to_segment.csv \\\n\t--output_dir\
      \ /output"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ct-based_neuroblastoma_tumour_detection_and_segmentation/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:20:51.076833Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ct-based_neuroblastoma_tumour_detection_and_segmentation/info-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: CT-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-022_T-01-02-005)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.3390/app11083508
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Usage
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - 2.0.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T12:09:16.704255Z'
  biotoolsCURIE: biotools:mr-based_glioblastoma_tumour_detection_and_segmentation
  biotoolsID: mr-based_glioblastoma_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: maria_beser@iislafe.es
    fundrefid: null
    gridid: null
    name: Maria Beser-Robles
    note: null
    orcidid: https://orcid.org/0000-0002-0072-5525
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Support
    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: 'The tool performs an automatic segmentation of the possible glioblastoma
    tumours on MRI images and its subregions: necrosis (Intratumoral necrotic core),
    edema (Peritumoral vasogenic edema), enhancing (Contrast-enhancing tumor region),
    total (Total tumor including edema and necrosis by a single model) and total-fused
    (Total tumor fusioning of necrosis+edema+enhancing). It applies preprocessing
    steps as skull stripping, intra-patient registration, z-score normalization, patching,
    among others. It takes DICOM images as input and generates tumoral masks in DICOM
    SEG or NIFTI formats.'
  documentation:
  - note: null
    type:
    - General
    url: https://pubmed.ncbi.nlm.nih.gov/38849632/
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/otrYTickHjDxnkP
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=8_OJPTQUKAw&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=22
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
      \ \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest\
      \ \\\n  --series-selector /input/config/series.csv \\\n  --target total \\\n\
      \  --emit-config true"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
      \ \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest\
      \ \\\n  --series-list '[{\"dataset_id\":\"DS001\",\"patient_id\":\"PAT001\"\
      ,\"study_id\":\"ST001\",\"series_path\":\"/input/DICOM/DS001/PAT001/ST001/T1_POST\"\
      }]' \\\n  --target total-fused \\\n  --emit-config true"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:20:39.690457Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/info-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: MR-based glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s11548-024-03205-z
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - 2.1.1
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:19:51.404419Z'
  biotoolsCURIE: biotools:mr-based_dipg_tumour_detection_and_segmentation
  biotoolsID: mr-based_dipg_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: matias_fernandez@iislafe.es
    fundrefid: null
    gridid: null
    name: Matias Fernandez-Paton
    note: null
    orcidid: https://orcid.org/0000-0001-9374-1411
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Support
    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Documentor
    - Support
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: The tool performs an automatic segmentation of the possible DIPG tumours
    on MR images. DIPG (Diffuse Intrinsic Pontine Glioma), or more recently, DMG (Diffuse
    Midline Glioma) is a H3 K27M–mutant pediatric brainstem cancer detected in T1W
    and Flair/T2-weighted magnetic resonance images. The tool includes a complete
    workflow from DICOM images to DICOM seg tumoral masks.
  documentation:
  - note: null
    type:
    - General
    url: https://link.springer.com/article/10.1007/s10278-025-01557-9
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/5CL2H8tyMDzFHex
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=f3DPS56z6oI&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=36
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
      \ \\\nharbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest\
      \ \\\n  --series-selector /input/config/series.csv"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input -v /path/to/output:/output\
      \ harbor.eucaim.cancerimage.eu/processing-tools/mr-based_dipg_tumour_detection_and_segmentation:latest\
      \ \\\n  --json-args '{\"dataset_id\":\"DS1\",\"patient_id\":\"P1\",\"study_id\"\
      :\"S1\",\"sequences\":{\"T1w\":\"/input/DICOM/DS1/P1/S1/T1\",\"FLAIR\":\"/input/DICOM/DS1/P1/S1/FLAIR\"\
      }}'"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:20:21.739269Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/info-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: MR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s10278-025-01557-9
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  validated: 0
  version:
  - 2.0.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:08:44.174795Z'
  biotoolsCURIE: biotools:mr-based_neuroblastoma_tumour_detection_and_segmentation
  biotoolsID: mr-based_neuroblastoma_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: dianaveigac@gmail.com
    fundrefid: null
    gridid: null
    name: Diana Veiga Canuto
    note: null
    orcidid: https://orcid.org/0000-0002-6048-2940
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Support
    - Documentor
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    - Documentor
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: 'This tool is specifically designed and validated for automated detection
    and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images
    (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs
    in NIFTI or DICOM SEG.


    TRAINING & VALIDATION COHORTS:


    Initial Development (Veiga-Canuto 2022):

    -Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).

    -Internal validation: 26 patients (median DSC 0.918 ± 0.067).

    -Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).

    -Mean age: 37.6 ± 39.3 months.

    -Median tumor volume: 116,518 mm³.


    External Validation (Veiga-Canuto 2023):

    -300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).

    -Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.

    -Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German
    Registry 62, others 12).

    -Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105),
    Canon (3).'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/tS2W8nb38Zs2ZzK
  - note: null
    type:
    - General
    url: https://www.mdpi.com/2072-6694/14/15/3648
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/44BxMSNpxwgsZiE
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=c7XOEGRA9aQ&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=12
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run --rm \\\n  -v \"<input_path>:/input\" \\\n  -v \"<output_path>:/output\"\
      \ \\\n  --gpus all \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0\
      \ \\\n  --mode dicom-seg \\\n  --series-selector /output/config/series_to_segment.csv\
      \ \\\n  --seg-series-number 2302001 \\\n  --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\"\
      \ \\\n  --seg-coordinating-center \"EUCAIM Consortium\" \\\n  --keep-nifti false"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:19:40.961989Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.3390/cancers14153648
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.3390/cancers15051622
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  validated: 0
  version:
  - 2.0.0
- accessibility: null
  additionDate: '2025-05-29T08:55:46.088021Z'
  biotoolsCURIE: biotools:denoising-inhomogeneity_correction_tool
  biotoolsID: denoising-inhomogeneity_correction_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: matias_fernandez@iislafe.es
    fundrefid: null
    gridid: null
    name: Matias Fernandez-Paton
    note: null
    orcidid: https://orcid.org/0000-0001-9374-1411
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Documentor
    - Support
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Documentor
    - Support
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: 'The tool is designed to perform a customisable image pre-processing
    to reduce noise and inhomogeneity field effect, thus improving image quality and
    reproducibility of radiomics features. This tool consists of two independent steps:
    one for denoising using one of the 5 integrated filters (Bilateral Filter, Anisotropic
    Diffusion Filter (ADF), Curvature Flow Filter (CFF), SUSAN and Non Local Means
    (NLM)), and another for the ANTs N4 and another for the ANT''s N4 bias correction
    filter. The parameter configuration of this tool has been optimised for TW1, T2W,
    DWI and DCE sequences in neuroblastoma (NB) and paediatric brain tumours, but
    it can also be configured with some of their parameters using a JSON parameter
    configuration file.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/wYJ7Fttnk6Dp7gc
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/oseiKoeFZqwoRCA
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=HkHqFGXGEbo&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=9
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run -it --rm --name container_name -v "<input_path>:/input" -v "<output_path>:/output"
      -v "<config_path>:/config" harbor.eucaim.cancerimage.eu/processing-tools/denoising_inhomogeneity_correction_tool:1.1.0
      --config /config/config.json
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processin-tools/denoising_inhomogeneity_correction_tool:1.1.0
      --paths /input/Dataset/Patient_1/Study/T1W /input/Dataset/Patient_2/Study/T2W
      --output /output --series_number 2000 --series_description_suffix "_harmonized"
      --denoising adf --conductance 0.5 --iterations 3 --time_step 0.0625 --n4 --bspline_size
      50 --n4_iterations 50 30 --shrink_factor 2
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:19:25.220262Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: null
  name: Denoising-Inhomogeneity Correction Tool (EUCAIM-SW-015_T-01-01-015)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s10278-021-00512-8
    metadata: null
    note: null
    pmcid: PMC8554919
    pmid: '34505958'
    type:
    - Primary
    version: null
  - doi: 10.1186/s41747-020-00150-9
    metadata: null
    note: null
    pmcid: PMC7125275
    pmid: '32246291'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-11-25T09:58:37.569343Z'
  biotoolsCURIE: biotools:ml_model_for_mr_series_categorisation
  biotoolsID: ml_model_for_mr_series_categorisation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: armago@alumni.uv.es
    fundrefid: null
    gridid: null
    name: Armando Gomis-Maya
    note: null
    orcidid: https://orcid.org/0000-0002-9527-8093
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: A tool based on artificial intelligence that is able to perform a categorisation
    of MRI series by using standardized DICOM tags. The categorisation includes the
    type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W,
    DCE, ...), the presence of fat suppression and the detection of non-relevant /
    junk series (e.g. localizers, calibrations, screenshots...).
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/rpm56rD5FfXAHyb
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/8r3CzyQXrd7ERFp
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=gudDCiuJIf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=11
  download: []
  editPermission:
    authors:
    - casopon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/ml_model_for_mr_series_categorisation:<version>\
      \ \\\n  --config-string \"{'output_name': 'classification_results.json'}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:19:08.404060Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication:
  - doi: 10.1186/s40537-025-01086-w
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-11-21T13:49:36.578343Z'
  biotoolsCURIE: biotools:time_coherence_tool
  biotoolsID: time_coherence_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Support
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  description: "Tool that aims to validate visually the chronological order and logical\
    \ consistency of dates associated with a patient's medical history. It generates\
    \ a timeline visualization for each patient from an Excel file and highlights\
    \ rule violations.\n \nStatus : Containerized"
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/M23wDa4RWXenzxX
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/9QbdWjnLBeMYSWR
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=j4J_UPQqYR4&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=10
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 'docker run -it --rm --name my-container -v "<input_path>:/input" -v "<output_path>:/output"
      harbor.eucaim.cancerimage.eu/processing-tools/time_coherence_tool:2.1.0 --config-string
      "{''data_file'': ''my_data.xlsx'', ''generate_pdf'': ''true''}"'
    input:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Data analysis
      uri: http://edamontology.org/operation_2945
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: SVG
        uri: http://edamontology.org/format_3604
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:18:38.027942Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Emerging
  name: Time Coherence Tool (EUCAIM-SW-001_T-01-01-001)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: casopon
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-04-15T17:42:40.968987Z'
  biotoolsCURIE: biotools:dicom_file_integrity_checker_by_gibi230
  biotoolsID: dicom_file_integrity_checker_by_gibi230
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Documentor
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: 'The tool performs a DICOM quality check in terms of correct number
    of files per sequence, corrupted files, precise directory hierarchy, separated
    dynamic series merging them, interest series filtering/selection by specific series
    description lists and diffusion sequence identification by b-values. It applies
    the desired changes to the dataset and generates a report containing information
    about the selected sequences, corrupted files, missing files and merged files.


    Status: Deployed'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/LAKqSQZY4Bjqz5W
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/EEqjraK574HrwMf
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=oUebkjLYeSs&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=3
  download:
  - note: EUCAIM user needed
    type: Container file
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
    version: 2.1.0
  editPermission:
    authors:
    - casopon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  -v \"<config_path>:/config\" \\\n\
      \  harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_file_integrity_checker:latest"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: For Data Holders (ingestion-tools)
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/dicom_file_integrity_checker:latest\
      \ \\\n  /app/entrypoint.sh --config-string \"{'QA': {'sequence_selection': ['ALL'],\
      \ 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: For Data Users (processing-tools)
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:16:18.033519Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  - note: Link to EUCAIM's Harbor for Data Holders
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
  - note: Link to EUCAIM's Harbor for Data Users
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab
  maturity: Mature
  name: DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - 2.0.0
  - 2.1.0
  - 2.1.1
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-28T23:59:16.112917Z'
  biotoolsCURIE: biotools:dicom-seg_annotation
  biotoolsID: dicom-seg_annotation
  collectionID:
  - eucaim
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: This module provides a command line tool to validate DICOM SEG files
    against predefined requirements specified in an Excel file. It contains components
    for finding relevant DICOM files, loading and parsing validation requests and
    applying validation rules. The main validation process checks each DICOM file
    for compliance with the Type 1, 1C, 2, 2C and 3 attributes specified in the requirements
    file. A detailed report is generated highlighting issues such as missing, invalid
    or conditionally required attributes, including file paths and affected DICOM
    tags. The tool is designed to ensure data integrity and compliance with DICOM
    standards.
  documentation:
  - note: null
    type:
    - General
    url: https://drive.eucaim.cancerimage.eu/s/i4D6iMeBCxxHGXz
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/PgS6HJ5pBTk8THW
  download: []
  editPermission:
    authors:
    - authEucaim
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologies
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-21T11:59:37.802307Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/annotation_tool/info-tab
  maturity: Mature
  name: DICOM-SEG Annotation
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: difoto
  publication: []
  relation:
  - biotoolsID: data_integration_quality_check_tool_diqct
    type: includedIn
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version:
  - '0.1'
next: ?page=2
previous: null
