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  description: The NLmCED (Non Local mean Coherence Enhancing Diffusion) filter is
    a denoising tool aimed to reduce Rician Noise in 3D MR images. It is a combination
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    tensor method with an estimator of Rician noise. The NLmCED filter can benefit
    from the noise reduction capabilities of the NLM filter while maintaining the
    edge-preserving characteristics of anisotropic diffusion.
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  function:
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    note: null
    operation:
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    - term: Data filtering
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    output:
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  lastUpdate: '2026-05-13T08:26:26.116424Z'
  license: CC-BY-NC-ND-4.0
  link:
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    type:
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nlmced/info-tab
  maturity: null
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  operatingSystem:
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  otherID: []
  owner: Feriel
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1002/mrm.28676
    metadata: null
    note: null
    pmcid: null
    pmid: null
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  relation: []
  toolType:
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  topic:
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  - term: MRI
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  - term: Medical imaging
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  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2026-05-13T06:42:26.772110Z'
  biotoolsCURIE: biotools:exomeflow
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    note: null
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    rorid: null
    typeEntity: Person
    typeRole:
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    url: https://pypi.org/project/exomeflow/
  description: 'ExomeFlow is a Python package that provides a complete, automated
    Whole Exome Sequencing (WES) analysis workflow from raw FASTQ files to functionally
    annotated variants in a single reproducible CLI command.


    It aims to be the standard high-level pipeline for WES analysis in Python, combining
    GATK best-practice variant calling, hard filtering, and ANNOVAR annotation into
    one modular, maintainable package. It handles cohort-level processing (multiple
    samples), checkpointing for resumable runs, structured logging, and parallel execution
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  - note: null
    type:
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    type: Software package
    url: https://pypi.org/project/exomeflow/
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  language:
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  - Bash
  lastUpdate: '2026-05-13T07:08:06.554344Z'
  license: Freeware
  link:
  - note: null
    type:
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    url: https://pypi.org/project/exomeflow/
  maturity: Emerging
  name: ExomeFlow
  operatingSystem:
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  otherID: []
  owner: robin_kumar
  publication: []
  relation:
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  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: DNA mutation
    uri: http://edamontology.org/topic_2533
  validated: 0
  version:
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  - 1.0.8
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  additionDate: '2026-05-13T05:45:59.510938Z'
  biotoolsCURIE: biotools:framexplore
  biotoolsID: framexplore
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Vidhu S Vijay
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      of FrameXplore.
    orcidid: https://orcid.org/0009-0009-1182-2089
    rorid: null
    typeEntity: Person
    typeRole:
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    url: https://github.com/Vidhusv
  description: FrameXplore is a Google Colab notebook that extends ColabFold to automatically
    identify and correct disulfide bonds in cysteine‑rich protein structures. After
    a standard ColabFold prediction, it extracts all cysteine residues, computes Cα–Cα
    and S–S distances, identifies true disulfide bonds using geometric cutoffs (Cα–Cα
    < 6.5 Å, S–S < 2.5 Å), writes a corrected PDB with proper CONECT records, and
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  documentation:
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    type:
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    url: https://github.com/Vidhusv/FRAMEXPLORER/blob/main/README.md
  download:
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    type: Source code
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  homepage_status: 0
  language:
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  lastUpdate: '2026-05-13T06:23:55.557041Z'
  license: MIT
  link:
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  - note: Report bugs, suggest features, or ask questions
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    metadata: null
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  topic:
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  additionDate: '2020-06-08T16:00:55Z'
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    fundrefid: null
    gridid: null
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    rorid: null
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  description: METALizer predicts the coordination geometry of metal ions in metalloproteins.
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    structure. The predicted coordination geometries and the observed metal interaction
    distances can be interactively compared to statistics calculated based on the
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  documentation:
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    type:
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    note: null
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  language: []
  lastUpdate: '2026-05-12T11:59:49.686219Z'
  license: Other
  link:
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    type:
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    url: https://proteins.plus
  - note: A web API to run METALizer calculations for protein structures stored in
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    type:
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  name: METALizer
  operatingSystem:
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  - Linux
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  otherID: []
  owner: ehrt
  publication:
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    metadata: null
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  - term: Sequence sites, features and motifs
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  - term: Protein structure analysis
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  - term: Drug discovery
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  - term: Data mining
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  - term: Bioinformatics
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  - term: Molecular interactions, pathways and networks
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  validated: 1
  version: []
- accessibility: null
  additionDate: '2026-05-12T09:59:14.748441Z'
  biotoolsCURIE: biotools:cycsim
  biotoolsID: cycsim
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  confidence_flag: null
  cost: null
  credit: []
  description: 'Long-read sequencing data contain context-dependent errors, where
    certain bases are more likely to be misread depending on their surrounding sequence.
    Most existing simulators introduce errors randomly, which overlooks these error
    biases and only approximates the overall error rate. CycSim takes a different
    approach by modeling errors in a k-mer–dependent manner, enabling more realistic
    and biologically accurate error simulation.


    CycSim is easy to train and supports all types of long-read sequencing data. It
    currently provides pre-trained models for BGI CycloneSEQ, PacBio HiFi, and Oxford
    Nanopore Q20 data. Users can also quickly train their own custom models using
    a BAM file of reads aligned to a reference genome.'
  documentation: []
  download: []
  editPermission:
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  homepage_status: 0
  language: []
  lastUpdate: '2026-05-12T09:59:33.536530Z'
  license: null
  link: []
  maturity: null
  name: CycSim
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  owner: jiang
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-05-07T14:37:06.887814Z'
  biotoolsCURIE: biotools:bigr_xnattools
  biotoolsID: bigr_xnattools
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  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Martijn PA Starmans
    note: null
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    note: null
    orcidid: null
    rorid: null
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  description: 'xnattools is a python package with a set of modules for performing
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    one standardized platform for running operations on XNAT servers. The package
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    thumbnail generation from dicom, DICOM header data collection, in bulk downloading
    of a project.'
  documentation: []
  download:
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    type: Source code
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  lastUpdate: '2026-05-12T09:58:09.783339Z'
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  - biotoolsID: xnat
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  toolType:
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  additionDate: '2026-05-10T14:17:21.546930Z'
  biotoolsCURIE: biotools:tsenat
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  description: TSENAT is a R package for quantifying and modeling isoform-usage complexity
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  documentation:
  - note: null
    type:
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  download:
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  description: GlyComboCLI is an open source command line interface for combinatorial
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    input:
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  additionDate: '2022-05-08T14:24:43.524310Z'
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  description: FLIRT is a Feature generation tooLkIt for weaRable daTa such as that
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  description: RepeatAfterMe is a package for the extension of repetitive DNA cores.
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        more methods to enhance performance. Our specific hybrid method, which combines
        a motif-based approach with a machine learning-based model, achieved a maximum
        AUROC of 0.98 with MCC 0.81 on an independent dataset. In this study, all
        models were trained and tested on 80 % of data using five-fold cross-validation
        and evaluated on the remaining 20 % of data called independent dataset. The
        evaluation of all methods on an independent dataset revealed that the method
        proposed in this study exhibited better performance than existing methods.
        To cater to the needs of the scientific community, we have developed a standalone
        software, pip package and web-based server ToxinPred3 (https://github.com/raghavagps/toxinpred3
        and https://webs.iiitd.edu.in/raghava/toxinpred3/).
      authors:
      - name: Rathore A.S.
      - name: Choudhury S.
      - name: Arora A.
      - name: Tijare P.
      - name: Raghava G.P.S.
      citationCount: 6
      date: '2024-09-01T00:00:00Z'
      journal: Computers in Biology and Medicine
      title: 'ToxinPred 3.0: An improved method for predicting the toxicity of peptides'
    note: null
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  description: MicroMiner assists in identifying single-residue substitutions in protein
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  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,
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    ligand properties such as electron density support and the validity of torsion
    angles.
  documentation:
  - note: null
    type:
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  function:
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    - data:
        term: Protein-ligand complex
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      format:
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      - term: SDF
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    note: null
    operation:
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    - term: Protein-ligand docking
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    - term: Protein geometry calculation
      uri: http://edamontology.org/operation_0249
    - term: Protein structure validation
      uri: http://edamontology.org/operation_0321
    output:
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        term: Protein structural quality report
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      format: []
    - data:
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      format: []
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/structureprofiler.html
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  language: []
  lastUpdate: '2026-05-05T08:29:40.642831Z'
  license: Other
  link:
  - note: A web service to run StructureProfiler calculations for protein structures
      stored in the Protein Data Bank.
    type:
    - Service
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  - note: A web API to run StructureProfiler calculations for protein structures stored
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    type:
    - Service
    url: https://proteins.plus/help/structurechecker_rest
  - note: Link to download the standalone tool from the NAOMI ChemBio Suite.
    type:
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    url: https://uhh.de/naomi
  maturity: Mature
  name: StructureProfiler
  operatingSystem:
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  publication:
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    metadata: null
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    type:
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    version: null
  relation: []
  toolType:
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  - Web service
  - Web API
  topic:
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    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: '2016-11-28T10:07:16Z'
  biotoolsCURIE: biotools:ppi
  biotoolsID: ppi
  collectionID:
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  confidence_flag: tool
  cost: Free of charge
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  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:
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    type:
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  function:
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      format:
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    note: Probability score for interface classification
    operation:
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      uri: http://edamontology.org/operation_2949
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    output:
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        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  homepage: https://proteins.plus/help/ppi
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  lastUpdate: '2026-05-05T08:29:02.104257Z'
  license: Other
  link:
  - note: A web service to run HyPPI calculations for protein structures stored in
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    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
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    metadata: null
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    type:
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    type:
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  relation: []
  toolType:
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  - Web service
  topic:
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  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-11-21T10:33:07Z'
  biotoolsCURIE: biotools:dogsitescorer
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  collectionID:
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  confidence_flag: tool
  cost: Free of charge
  credit:
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  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:
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    type:
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  download: []
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  function:
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    - data:
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      format:
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      - term: SDF
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    - data:
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      format: []
    note: Computational detection of protein binding pockets Protein binding pockets
      Property statistics of all protein binding pockets
    operation:
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      uri: http://edamontology.org/operation_1777
    - term: Ligand-binding site prediction
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    - term: Protein structure analysis
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    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
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        uri: http://edamontology.org/format_1476
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsitescorer.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-05-05T08:27:41.055032Z'
  license: Other
  link:
  - note: A web service to run DoGSiteScorer calculations for protein structures stored
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    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:
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  maturity: Mature
  name: DoGSiteScorer
  operatingSystem:
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  otherID: []
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  publication:
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    metadata: null
    note: null
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    type:
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    version: null
  - doi: 10.1093/bioinformatics/bts310
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    type:
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  relation: []
  toolType:
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  topic:
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  - 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:
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  confidence_flag: null
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  credit:
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    fundrefid: null
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    orcidid: null
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    typeRole:
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  - email: software.zbh@uni-hamburg.de
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  - email: null
    fundrefid: null
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  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:
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    type: Binaries
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    version: null
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  function:
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    - data:
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    note: null
    operation:
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        uri: http://edamontology.org/format_1476
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsite3.html
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  language: []
  lastUpdate: '2026-05-05T08:26:36.616400Z'
  license: Other
  link:
  - note: A web service to run DoGSite3 calculations for protein structures stored
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    type:
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  - note: A web API to run DoGSite3 calculations for protein structures stored in
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    type:
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  - note: Link to download the standalone tool from the NAOMI ChemBio Suite.
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  maturity: Mature
  name: DoGSite3
  operatingSystem:
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  otherID: []
  owner: ehrt
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: '37130052'
    type:
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    version: null
  relation:
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  toolType:
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  topic:
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  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Molecular modelling
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  - term: Protein properties
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  validated: 0
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- accessibility: null
  additionDate: '2021-01-18T10:36:05Z'
  biotoolsCURIE: biotools:geomine
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  credit:
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  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
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    pockets (based on DoGSite3) for query generation. The query management is based
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  documentation:
  - note: null
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  download: []
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    - data:
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    note: null
    operation:
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    - term: Database search
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    output:
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        uri: http://edamontology.org/format_1476
  homepage: https://www.zbh.uni-hamburg.de/forschung/amd/software/geomine.html
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  language: []
  lastUpdate: '2026-05-05T08:24:36.661849Z'
  license: Other
  link:
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    type:
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  - note: A web API to run GeoMine calculations for protein structures stored in the
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    type:
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  maturity: Mature
  name: GeoMine
  operatingSystem:
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  otherID: []
  owner: ehrt
  publication:
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    metadata: null
    note: null
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    type:
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    metadata: null
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    type:
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  - doi: 10.1021/acs.jmedchem.1c01046
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    type:
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  - doi: 10.1007/s10822-024-00563-3
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    type:
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  relation:
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  topic:
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  - 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: '2020-06-08T16:17:43Z'
  biotoolsCURIE: biotools:warpp
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  collectionID:
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  cost: Free of charge (with restrictions)
  credit:
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    fundrefid: null
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    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
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    typeRole:
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    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
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    type:
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  toolType:
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  description: JAMDA enables the preparation of individual protein structures and
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  description: Protoss is a fully automated hydrogen atom placement tool for protein-ligand
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  description: PoseEdit automatically generates 2D diagrams of protein-ligand complexes,
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  description: PoseView automatically generates 2D diagrams of protein-ligand complexes,
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  - 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
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  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-11-28T10:07:17Z'
  biotoolsCURIE: biotools:edia
  biotoolsID: edia
  collectionID:
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  - 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: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    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:
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    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:
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    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:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
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        term: Protein structure
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      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
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      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: Score for structure quality assessment on a global or atomistic level
    operation:
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    - term: Protein model 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:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/ediascorer.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-05-05T08:14:04.701167Z'
  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
  - Linux
  - Mac
  otherID: []
  owner: ehrt
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: '28981269'
    type:
    - Primary
    version: null
  relation:
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  toolType:
  - Command-line tool
  - Web service
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  topic:
  - term: Structure analysis
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  - 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: '2025-12-15T10:42:55.566760Z'
  biotoolsCURIE: biotools:lifesoaks
  biotoolsID: lifesoaks
  collectionID:
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  - 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:
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    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
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    name: NAOMI ChemBio Suite Support
    note: Primary Contact for Standalone Tool Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
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  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:
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    type: group
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  - Tools
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  function:
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    input:
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      format:
      - term: PDB
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    - data:
        term: Protein-ligand complex
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      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: null
    operation:
    - term: Protein property calculation
      uri: http://edamontology.org/operation_0250
    output:
    - data:
        term: Protein structure report
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      format: []
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/lifesoaks.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-05-05T08:12:57.342788Z'
  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
  - Linux
  - Mac
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1107/S205979832300582X
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web service
  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: '2024-03-05T01:49:53.830800Z'
  biotoolsCURIE: biotools:gsc_genotype_sparse_compression
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  description: Genotype Sparse Compression (GSC) is an advanced tool for lossless
    compression of VCF files, designed to efficiently store and manage VCF files in
    a compressed format. It accepts VCF/BCF files as input and utilizes advanced compression
    techniques to significantly reduce storage requirements while ensuring fast query
    capabilities. In our study, we successfully compressed the VCF files from the
    1000 Genomes Project (1000Gpip3), consisting of 2504 samples and 80 million variants,
    from an uncompressed VCF file of 803.70GB to approximately 1GB.
  documentation: []
  download: []
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  license: null
  link: []
  maturity: null
  name: GSC (Genotype Sparse Compression)
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  relation: []
  toolType: []
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  validated: 0
  version:
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- accessibility: null
  additionDate: '2022-07-04T14:39:20.644374Z'
  biotoolsCURIE: biotools:hifiasm
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  description: 'Hifiasm: a haplotype-resolved assembler for accurate Hifi reads'
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  - note: null
    type:
    - General
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  download: []
  editPermission:
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    output: []
  homepage: https://github.com/chhylp123/hifiasm
  homepage_status: 0
  language:
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  - C++
  lastUpdate: '2026-05-05T08:11:43.608451Z'
  license: MIT
  link: []
  maturity: null
  name: Hifiasm
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  otherID: []
  owner: alexcorm
  publication:
  - doi: 10.1038/s41592-020-01056-5
    metadata:
      abstract: Haplotype-resolved de novo assembly is the ultimate solution to the
        study of sequence variations in a genome. However, existing algorithms either
        collapse heterozygous alleles into one consensus copy or fail to cleanly separate
        the haplotypes to produce high-quality phased assemblies. Here we describe
        hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence
        reads to faithfully represent the haplotype information in a phased assembly
        graph. Unlike other graph-based assemblers that only aim to maintain the contiguity
        of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes.
        This feature enables the development of a graph trio binning algorithm that
        greatly advances over standard trio binning. On three human and five nonhuman
        datasets, including California redwood with a ~30-Gb hexaploid genome, we
        show that hifiasm frequently delivers better assemblies than existing tools
        and consistently outperforms others on haplotype-resolved assembly.
      authors:
      - name: Cheng H.
      - name: Concepcion G.T.
      - name: Feng X.
      - name: Zhang H.
      - name: Li H.
      citationCount: 1739
      date: '2021-02-01T00:00:00Z'
      journal: Nature Methods
      title: Haplotype-resolved de novo assembly using phased assembly graphs with
        hifiasm
    note: null
    pmcid: PMC7961889
    pmid: '33526886'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version:
  - 0.16.1
- accessibility: null
  additionDate: '2022-08-11T10:07:55.182946Z'
  biotoolsCURIE: biotools:cb-dock2
  biotoolsID: cb-dock2
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: cao@scu.edu.cn
    fundrefid: null
    gridid: null
    name: Yang Cao
    note: null
    orcidid: https://orcid.org/0000-0002-1925-2123
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Yang Liu
    note: null
    orcidid: https://orcid.org/0000-0002-2517-9436
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: CB-Dock2  is an improved version of the CB-Dock server for protein-ligand
    blind docking, integrating cavity detection, docking and homologous template fitting.
  documentation:
  - note: null
    type:
    - User manual
    url: https://cadd.labshare.cn/cb-dock2/php/manual.php
  download: []
  editPermission:
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    type: public
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  function:
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    input: []
    note: null
    operation:
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    - term: Binding site prediction
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    - term: Protein-protein docking
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    - term: Small molecule design
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    output: []
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  language: []
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  link: []
  maturity: null
  name: CB-Dock2
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  owner: ismail1
  publication:
  - doi: 10.1093/nar/gkac394
    metadata:
      abstract: Protein-ligand blind docking is a powerful method for exploring the
        binding sites of receptors and the corresponding binding poses of ligands.
        It has seen wide applications in pharmaceutical and biological researches.
        Previously, we proposed a blind docking server, CB-Dock, which has been under
        heavy use (over 200 submissions per day) by researchers worldwide since 2019.
        Here, we substantially improved the docking method by combining CB-Dock with
        our template-based docking engine to enhance the accuracy in binding site
        identification and binding pose prediction. In the benchmark tests, it yielded
        the success rate of ∼85% for binding pose prediction (RMSD < 2.0 Å), which
        outperformed original CB-Dock and most popular blind docking tools. This updated
        docking server, named CB-Dock2, reconfigured the input and output web interfaces,
        together with a highly automatic docking pipeline, making it a particularly
        efficient and easy-to-use tool for the bioinformatics and cheminformatics
        communities. The web server is freely available at https://cadd.labshare.cn/cb-dock2/.
      authors:
      - name: Liu Y.
      - name: Yang X.
      - name: Gan J.
      - name: Chen S.
      - name: Xiao Z.-X.
      - name: Cao Y.
      citationCount: 408
      date: '2022-07-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'CB-Dock2: improved protein-ligand blind docking by integrating cavity
        detection, docking and homologous template fitting'
    note: null
    pmcid: PMC9252749
    pmid: '35609983'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Medicinal chemistry
    uri: http://edamontology.org/topic_0209
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-03-25T16:29:45Z'
  biotoolsCURIE: biotools:evolview
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  collectionID: []
  confidence_flag: null
  cost: null
  credit:
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    fundrefid: null
    gridid: null
    name: Evolview Team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Web server for displaying, managing and customizing phylogenetic trees.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/evolgeniusteam/EvolviewDocumentation
  download: []
  editPermission:
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    - term: Phylogenetic tree annotation
      uri: http://edamontology.org/operation_0558
    - term: Phylogenetic tree editing
      uri: http://edamontology.org/operation_0326
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Phylogenetic tree reconstruction
      uri: http://edamontology.org/operation_3478
    output: []
  homepage: http://www.evolgenius.info/evolview.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-05-05T08:11:14.177108Z'
  license: null
  link: []
  maturity: null
  name: EvolView
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: user.1777699184
  publication:
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    metadata:
      abstract: 'EvolView is a web application for visualizing, annotating and managing
        phylogenetic trees. First, EvolView is a phylogenetic tree viewer and customization
        tool; it visualizes trees in various formats, customizes them through built-in
        functions that can link information from external datasets, and exports the
        customized results to publication-ready figures. Second, EvolView is a tree
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        trees and datasets. To make EvolView easy to use, it is equipped with an intuitive
        user interface. With a free account, users can save data and manipulations
        on the EvolView server. EvolView is freely available at: http://www.evolgenius.info/evolview.html.
        © 2012 The Author(s).'
      authors:
      - name: Zhang H.
      - name: Gao S.
      - name: Lercher M.J.
      - name: Hu S.
      - name: Chen W.-H.
      citationCount: 361
      date: '2012-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: EvolView, an online tool for visualizing, annotating and managing phylogenetic
        trees
    note: null
    pmcid: PMC3394307
    pmid: '22695796'
    type: []
    version: null
  - doi: 10.1093/nar/gkw370
    metadata:
      abstract: 'Evolview is an online visualization and management tool for customized
        and annotated phylogenetic trees. It allows users to visualize phylogenetic
        trees in various formats, customize the trees through built-in functions and
        user-supplied datasets and export the customization results to publication-ready
        figures. Its ''dataset system'' contains not only the data to be visualized
        on the tree, but also ''modifiers'' that control various aspects of the graphical
        annotation. Evolview is a single-page application (like Gmail); its carefully
        designed interface allows users to upload, visualize, manipulate and manage
        trees and datasets all in a single webpage. Developments since the last public
        release include a modern dataset editor with keyword highlighting functionality,
        seven newly added types of annotation datasets, collaboration support that
        allows users to share their trees and datasets and various improvements of
        the web interface and performance. In addition, we included eleven new ''Demo''
        trees to demonstrate the basic functionalities of Evolview, and five new ''Showcase''
        trees inspired by publications to showcase the power of Evolview in producing
        publication-ready figures. Evolview is freely available at: http://www.evolgenius.info/evolview/.'
      authors:
      - name: He Z.
      - name: Zhang H.
      - name: Gao S.
      - name: Lercher M.J.
      - name: Chen W.-H.
      - name: Hu S.
      citationCount: 480
      date: '2016-07-08T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'Evolview v2: an online visualization and management tool for customized
        and annotated phylogenetic trees'
    note: null
    pmcid: PMC4987921
    pmid: '27131786'
    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
  validated: 1
  version:
  - '2'
- accessibility: null
  additionDate: '2026-02-22T13:38:54.361681Z'
  biotoolsCURIE: biotools:clipkit
  biotoolsID: clipkit
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: jlsteenwyk@berkeley.edu
    fundrefid: null
    gridid: null
    name: Jacob L Steenwyk
    note: null
    orcidid: https://orcid.org/0000-0002-8436-595X
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: ClipKIT in the browser provides a web-based application for fast online
    trimming of multiple sequence alignments, enhancing accessibility for phylogenetics
    research. It uses cloud-based resources to efficiently trim alignments while retaining
    phylogenetically informative sites.
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://clipkit.genomelybio.com/#/terms
  - note: null
    type:
    - User manual
    url: https://clipkit.genomelybio.com/#/help
  download: []
  editPermission:
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    type: group
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    output: []
  homepage: https://clipkit.genomelybio.com
  homepage_status: 0
  language: []
  lastUpdate: '2026-05-05T08:11:09.988646Z'
  license: null
  link: []
  maturity: null
  name: ClipKIT in the browser
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1093/NAR/GKAF325
    metadata: null
    note: null
    pmcid: PMC12230650
    pmid: '40260744'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-05-05T06:03:45.867892Z'
  biotoolsCURIE: biotools:slow5-dorado
  biotoolsID: slow5-dorado
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Fork of dorado (high-performance, easy-to-use, open source analysis
    engine for Oxford Nanopore reads) that support S/BLOW5
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format: []
    note: null
    operation:
    - term: Base-calling
      uri: http://edamontology.org/operation_3185
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
  homepage: https://github.com/hiruna72/slow5-dorado
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-05-05T06:03:45.870767Z'
  license: Other
  link: []
  maturity: null
  name: slow5-dorado
  operatingSystem:
  - Linux
  otherID: []
  owner: veitveit11
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Long-read sequencing
    uri: http://edamontology.org/topic_4056
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 1.1.1
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