count: 278
list:
- accessibility: Open access
  additionDate: '2025-07-14T08:21:28.942611Z'
  biotoolsCURIE: biotools:UniversalMer
  biotoolsID: UniversalMer
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: UniversalMer is a k-mer counting tool for multiple size of k at once.
    It is available for DNA, RNA, and protein sequences. The program counts and summarizes
    the exact frequency of all k-mers from 1-mer to a user-defined maximum length
    (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in
    seconds. This program is designed for bioinformatics researchers and scientists.
  documentation: []
  download:
  - note: null
    type: Command-line specification
    url: https://sourceforge.net/projects/universal-mer/
    version: '2.0'
  editPermission:
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  elixirNode:
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  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    note: null
    operation:
    - term: k-mer counting
      uri: http://edamontology.org/operation_3472
    output:
    - data:
        term: Base word frequencies table
        uri: http://edamontology.org/data_1266
      format: []
    - data:
        term: Base frequencies table
        uri: http://edamontology.org/data_1265
      format: []
    - data:
        term: Text
        uri: http://edamontology.org/data_3671
      format: []
  homepage: https://ugrammer.github.io
  homepage_status: 0
  language:
  - C++
  - C
  lastUpdate: '2025-07-14T08:21:28.944946Z'
  license: Freeware
  link:
  - note: null
    type:
    - Mirror
    url: https://sourceforge.net/projects/universal-mer/
  maturity: Emerging
  name: UniversalMer
  operatingSystem:
  - Windows
  - Mac
  otherID: []
  owner: Ugrammer
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2022-02-07T23:41:36.733362Z'
  biotoolsCURIE: biotools:proteinprompt
  biotoolsID: proteinprompt
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: rene.staritzbichler@medizin.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: René Staritzbichler
    note: null
    orcidid: https://orcid.org/0000-0002-6719-2997
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Peter W. Hildebrand
    note: null
    orcidid: https://orcid.org/0000-0003-0063-1104
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Sebastian Canzler
    note: null
    orcidid: https://orcid.org/0000-0001-7935-9582
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Markus Fischer
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: David Ulbricht
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nikola Ristic
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A webserver for predicting protein-protein interactions.
  documentation: []
  download: []
  editPermission:
    authors:
    - andleeb
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    note: null
    operation:
    - term: Protein interaction prediction
      uri: http://edamontology.org/operation_2492
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Protein-protein binding site prediction
      uri: http://edamontology.org/operation_2464
    output: []
  homepage: http://proteinformatics.org/ProteinPrompt
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-02T08:39:17.251278Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.hzdr.de/proteinprompt/ProteinPrompt
  maturity: null
  name: ProteinPrompt
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1101/2021.09.03.458859
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Protein interaction experiment
    uri: http://edamontology.org/topic_3957
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-02-28T15:04:33.594183Z'
  biotoolsCURIE: biotools:prolfquapp
  biotoolsID: prolfquapp
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A command-line tool for differential expression analysis in quantitative
    proteomics
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/prolfqua/prolfquapp/blob/master/README.md
  download:
  - note: null
    type: Downloads page
    url: https://github.com/prolfqua/prolfquapp/releases/tag/0.1.6
    version: 0.1.6
  editPermission:
    authors:
    - thatmariia
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: './prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis
      -s DIANN

      # and again you run the version within the docker container with

      # ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y
      config.yaml -w NameOfAnalysis -s DIANN'
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Differential protein expression profiling
      uri: http://edamontology.org/operation_3741
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://github.com/prolfqua/prolfquapp
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-03-28T10:18:25.715685Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/prolfqua/prolfquapp
  - note: null
    type:
    - Issue tracker
    url: https://github.com/prolfqua/prolfquapp/issues
  maturity: Emerging
  name: prolfquapp
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1021/acs.jproteome.4c00911
    metadata:
      abstract: Mass spectrometry is a cornerstone of quantitative proteomics, enabling
        relative protein quantification and differential expression analysis (DEA)
        of proteins. As experiments grow in complexity, involving more samples, groups,
        and identified proteins, interactive differential expression analysis tools
        become impractical. The prolfquapp addresses this challenge by providing a
        command-line interface that simplifies DEA, making it accessible to nonprogrammers
        and seamlessly integrating it into workflow management systems. Prolfquapp
        streamlines data processing and result visualization by generating dynamic
        HTML reports that facilitate the exploration of differential expression results.
        These reports allow for investigating complex experiments, such as those involving
        repeated measurements or multiple explanatory variables. Additionally, prolfquapp
        supports various output formats, including XLSX files, SummarizedExperiment
        objects and rank files, for further interactive analysis using spreadsheet
        software, the exploreDE Shiny application, or gene set enrichment analysis
        software, respectively. By leveraging advanced statistical models from the
        prolfqua R package, prolfquapp offers a user-friendly, integrated solution
        for large-scale quantitative proteomics studies, combining efficient data
        processing with insightful, publication-ready outputs.
      authors:
      - name: Wolski W.E.
      - name: Grossmann J.
      - name: Schwarz L.
      - name: Leary P.
      - name: Turker C.
      - name: Nanni P.
      - name: Schlapbach R.
      - name: Panse C.
      citationCount: 0
      date: '2025-02-07T00:00:00Z'
      journal: Journal of Proteome Research
      title: prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential
        Expression Analysis in Quantitative Proteomics
    note: null
    pmcid: null
    pmid: null
    type: []
    version: 0.0.6
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version:
  - 0.1.6
- accessibility: Open access
  additionDate: '2025-03-17T14:56:35.753220Z'
  biotoolsCURIE: biotools:ddgemb
  biotoolsID: ddgemb
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA-BOLOGNA
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.biocomp.unibo.it
  - email: castrense.savojardo2@unibo.it
    fundrefid: null
    gridid: null
    name: Castrense Savojardo
    note: null
    orcidid: https://orcid.org/0000-0002-7359-0633
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    - Developer
    - Primary contact
    url: null
  description: Predicting the impact of mutations on protein stability from sequence
    using protein language models
  documentation:
  - note: null
    type:
    - General
    url: https://ddgemb.biocomp.unibo.it/help/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Rare Diseases
  - 3D-BioInfo
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format: []
    note: null
    operation: []
    output:
    - data:
        term: Protein report
        uri: http://edamontology.org/data_0896
      format: []
  homepage: https://ddgemb.biocomp.unibo.it
  homepage_status: 0
  language: []
  lastUpdate: '2025-03-17T15:08:51.796427Z'
  license: null
  link: []
  maturity: Mature
  name: DDGemb
  operatingSystem: []
  otherID: []
  owner: ELIXIR-ITA-BOLOGNA
  publication:
  - doi: 10.1093/bioinformatics/btaf019
    metadata:
      abstract: 'Motivation: The knowledge of protein stability upon residue variation
        is an important step for functional protein design and for understanding how
        protein variants can promote disease onset. Computational methods are important
        to complement experimental approaches and allow a fast screening of large
        datasets of variations. Results: In this work, we present DDGemb, a novel
        method combining protein language model embeddings and transformer architectures
        to predict protein ΔΔG upon both single- and multi-point variations. DDGemb
        has been trained on a high-quality dataset derived from literature and tested
        on available benchmark datasets of single- and multi-point variations. DDGemb
        performs at the state of the art in both single- and multi-point variations.'
      authors:
      - name: Savojardo C.
      - name: Manfredi M.
      - name: Martelli P.L.
      - name: Casadio R.
      citationCount: 0
      date: '2025-01-01T00:00:00Z'
      journal: Bioinformatics
      title: 'DDGemb: predicting protein stability change upon single- and multi-point
        variations with embeddings and deep learning'
    note: null
    pmcid: PMC11783275
    pmid: '39799516'
    type:
    - Primary
    version: null
  relation: []
  toolType: []
  topic:
  - term: Protein folding, stability and design
    uri: http://edamontology.org/topic_0130
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 0
  version:
  - '1'
- accessibility: Open access
  additionDate: '2025-03-04T16:25:28.372680Z'
  biotoolsCURIE: biotools:pep-fold4
  biotoolsID: pep-fold4
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: julien.rey@u-paris.fr
    fundrefid: null
    gridid: null
    name: Julien Rey
    note: null
    orcidid: https://orcid.org/0000-0002-3050-511X
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    - Developer
    - Primary contact
    url: null
  - email: samuel.muriail@u-paris.fr
    fundrefid: null
    gridid: null
    name: Samuel Murail
    note: null
    orcidid: https://orcid.org/0000-0002-3842-5333
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Sjoerd de Vries
    note: null
    orcidid: https://orcid.org/0000-0002-7701-3454
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: philippe.derreumaux@ibpc.fr
    fundrefid: null
    gridid: null
    name: Philippe Derreumaux
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: pierre.tuffery@inserm.fr
    fundrefid: null
    gridid: null
    name: Pierre Tufféry
    note: null
    orcidid: https://orcid.org/0000-0003-1033-9895
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: PEP-FOLD4 is a fast and accurate structure prediction tool for peptides
    of up to 40 amino acids in aqueous solutions. Unlike many machine-learning approaches
    (e.g., AlphaFold2, TrRosetta, RaptorX), it integrates the Debye-Hückel formalism
    for charged side-chain interactions with a Mie potential for intramolecular forces.
    Based on a coarse-grained representation, PEP-FOLD4 performs competitively on
    well-structured peptides and shows significant improvements for poly-charged peptides,
    making it particularly useful for studying pH- and salt-dependent conformations.
  documentation:
  - note: null
    type:
    - User manual
    url: https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4/
  download:
  - note: Source code and recipe for docker images allowing to run PEP-FOLD4 locally.
      All repository content is covered by a non-commercial license agreement and
      may be used for non-commercial and internal research purposes only.
    type: Source code
    url: https://owncloud.rpbs.univ-paris-diderot.fr/owncloud/index.php/s/7NHDSJXiQA0V2zy
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - France
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    note: null
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    - term: Ab initio structure prediction
      uri: http://edamontology.org/operation_0476
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDB database entry format
        uri: http://edamontology.org/format_1475
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format: []
  homepage: https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-03-05T16:21:19.399517Z'
  license: null
  link:
  - note: Link to the PEP-FOLD4 web page service
    type:
    - Service
    url: https://mobyle2.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD4
  maturity: Mature
  name: PEP-FOLD4
  operatingSystem: []
  otherID: []
  owner: nchevrollier
  publication:
  - doi: 10.1093/nar/gkad376
    metadata:
      abstract: Accurate and fast structure prediction of peptides of less 40 amino
        acids in aqueous solution has many biological applications, but their conformations
        are pH-and salt concentration-dependent. In this work, we present PEP-FOLD4
        which goes one step beyond many machine-learning approaches, such as AlphaFold2,
        TrRosetta and RaptorX. Adding the Debye-Hueckel formalism for charged-charged
        side chain interactions to a Mie formalism for all intramolecular (backbone
        and side chain) interactions, PEP-FOLD4, based on a coarse-grained representation
        of the peptides, performs as well as machine-learning methods on well-structured
        peptides, but displays significant improvements for poly-charged peptides.
        PEP-FOLD4 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4.
        This server is free and there is no login requirement.
      authors:
      - name: Rey J.
      - name: Murail S.
      - name: De Vries S.
      - name: Derreumaux P.
      - name: Tuffery P.
      citationCount: 39
      date: '2023-07-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'PEP-FOLD4: A pH-dependent force field for peptide structure prediction
        in aqueous solution'
    note: null
    pmcid: PMC10320157
    pmid: '37166962'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Computational chemistry
    uri: http://edamontology.org/topic_3332
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-01-31T17:19:47.094256Z'
  biotoolsCURIE: biotools:proteomaker
  biotoolsID: proteomaker
  collectionID:
  - Proteomics
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: ProteoMaker is a platform for the generation of an in-silico bottom-up
    proteomics data set with a ground truth on the level of proteoforms.
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/computproteomics/ProteoMaker
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Simulated gene expression data generation
      uri: http://edamontology.org/operation_3566
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Proteolytic digest
        uri: http://edamontology.org/data_1238
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: YAML
        uri: http://edamontology.org/format_3750
    - data:
        term: Statistical estimate score
        uri: http://edamontology.org/data_0951
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/computproteomics/ProteoMaker
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-01-31T17:19:47.096981Z'
  license: MIT
  link:
  - note: Web application
    type:
    - Service
    url: https://computproteomics.bmb.sdu.dk/app_direct/ProteoMaker
  maturity: Mature
  name: ProteoMaker
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: veitveit11
  publication: []
  relation: []
  toolType:
  - Library
  - Web application
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Simulation experiment
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    name: Vedran Kasalica
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  - email: null
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    name: Anna-Lena Lamprecht
    note: null
    orcidid: https://orcid.org/0000-0003-1953-5606
    rorid: null
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  description: shic is a collection of shims for use in automated workflow composition
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  homepage: https://github.com/magnuspalmblad/shic
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  language: []
  lastUpdate: '2025-01-16T16:39:33.218764Z'
  license: MIT
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    type:
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  biotoolsCURIE: biotools:phiembed
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  collectionID: []
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  cost: Free of charge
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    fundrefid: null
    gridid: null
    name: Mark Edward M. Gonzales
    note: Research Assistant, Bioinformatics Lab, Advanced Research Institute for
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    fundrefid: null
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    name: Jennifer C. Ureta
    note: Faculty, Bioinformatics Lab, Advanced Research Institute for Informatics,
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    fundrefid: null
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    name: Anish M.S. Shrestha
    note: Head, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing
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  description: PHIEmbed is a phage-host interaction prediction tool that uses protein
    language models to represent the receptor-binding proteins of phages. It presents
    improvements over using handcrafted (manually feature-engineered) sequence properties
    and eliminates the need to manually extract and select features from phage sequences.
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  - note: null
    type:
    - Installation instructions
    - Quick start guide
    - Citation instructions
    - Command-line options
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    note: Predicts the host genus of a phage given its receptor-binding protein sequences
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    metadata:
      abstract: With the growing interest in using phages to combat antimicrobial
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        been explored to help shortlist candidate phages. Most existing models consider
        entire proteomes and rely on manual feature engineering, which poses difficulty
        in selecting the most informative sequence properties to serve as input to
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        phage’s receptor-binding proteins, which are known to be the key machinery
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      - name: Ureta J.C.
      - name: Shrestha A.M.S.
      citationCount: 2
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      journal: PLoS ONE
      title: Protein embeddings improve phage-host interaction prediction
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  - term: Computational biology
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  - term: Virology
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  description: Prediction of MHC class I binding peptides.
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  description: Medium-chain dehydrogenases/reductases database.
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  description: Disorder/order prediction for proteins.
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    url: null
  - email: null
    fundrefid: null
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    name: Tatyana Goldberg
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    name: Technische Universität München
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  description: Display multiple-sequence alignment. The tool is also available as
    R/BioConductor interface to the multiple sequence alignment algorithms ClustalW,
    ClustalOmega, and Muscle. All three algorithms are integrated in the package,
    therefore, they do not depend on any external software tools and are available
    for all major platforms.
  documentation:
  - note: null
    type:
    - Terms of use
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  - note: null
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  - note: null
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  description: Multiple sequence alignment.
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  - note: null
    type:
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  - note: null
    type:
    - General
    url: http://www.uniprot.org/help/sequence-alignments
  - note: null
    type:
    - Terms of use
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  function:
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    input:
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      format: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Sequence alignment
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      format: []
  homepage: http://www.uniprot.org/align
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  lastUpdate: '2024-11-25T15:19:23.003433Z'
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  name: UniProt Align
  operatingSystem:
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  - Windows
  - Mac
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  owner: EMBL-EBI
  publication:
  - doi: 10.1093/nar/gku989
    metadata: null
    note: null
    pmcid: PMC4384041
    pmid: '25348405'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2015-01-22T11:49:01Z'
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    name: Jan Kosinski
    note: null
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    url: null
  description: 'At MODORAMA two applications can be run: MODexplorer, an integrated
    tool for exploring protein sequence, structure and function relationships, and
    MODalign, a rich alignment editor to improve target-template alignments'
  documentation:
  - note: null
    type:
    - General
    url: http://modorama.org/
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  function:
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    input:
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    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Sequence-structure alignment
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      format: []
    note: 'MODexplorer: Explores sequence, structure and function relationships in
      protein families and selects templates and perform homology modeling; MODalign:
      displays, evaluates and edits alignments for comparative (homology) modeling'
    operation:
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    - term: Sequence alignment refinement
      uri: http://edamontology.org/operation_2089
    - term: Protein structure prediction
      uri: http://edamontology.org/operation_0474
    output: []
  homepage: http://modorama.org
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T15:00:26.069732Z'
  license: null
  link: []
  maturity: null
  name: MODORAMA
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  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-ITA-SAPIENZA
  publication:
  - doi: 10.1093/bioinformatics/btt062
    metadata: null
    note: null
    pmcid: PMC3605600
    pmid: '23396123'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/bts070
    metadata: null
    note: null
    pmcid: PMC3315710
    pmid: '22308148'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2015-12-07T13:03:43Z'
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    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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  description: A hidden Markov model for GPCR detection.
  documentation:
  - note: null
    type:
    - General
    url: http://gpcrhmm.sbc.su.se/instructions.html
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  function:
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    input:
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      format: []
    note: null
    operation:
    - term: Prediction and recognition
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    output:
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        term: Protein features
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      format: []
  homepage: http://gpcrhmm.sbc.su.se/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:55:26.899358Z'
  license: null
  link: []
  maturity: null
  name: GPCRHMM
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  - Windows
  - Mac
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  owner: mikael.borg@bils.se
  publication:
  - doi: 10.1110/ps.051745906
    metadata: null
    note: null
    pmcid: PMC2249772
    pmid: '16452613'
    type:
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    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2018-06-18T09:30:36Z'
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    note: null
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    typeEntity: Person
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    url: null
  description: Symmetric protein docking for oligomers with Cn or Dn symmetry from
    the structure or sequence of a subunit molecule.
  documentation:
  - note: null
    type:
    - General
    url: http://huanglab.phys.hust.edu.cn/hsymdock/help.html
  download: []
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  function:
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    note: null
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  homepage: http://huanglab.phys.hust.edu.cn/hsymdock/
  homepage_status: 0
  language:
  - PHP
  lastUpdate: '2024-11-25T14:41:44.638481Z'
  license: null
  link: []
  maturity: null
  name: HSYMDOCK
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  - Mac
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  owner: aotamendi.1
  publication:
  - doi: 10.1093/nar/gky398
    metadata:
      abstract: A major subclass of protein-protein interactions is formed by homo-oligomers
        with certain symmetry. Therefore, computational modeling of the symmetric
        protein complexes is important for understanding the molecular mechanism of
        related biological processes. Although several symmetric docking algorithms
        have been developed for Cn symmetry, few docking servers have been proposed
        for Dn symmetry. Here, we present HSYMDOCK, a web server of our hierarchical
        symmetric docking algorithm that supports both Cn and Dn symmetry. The HSYMDOCK
        server was extensively evaluated on three benchmarks of symmetric protein
        complexes, including the 20 CASP11-CAPRI30 homo-oligomer targets, the symmetric
        docking benchmark of 213 Cn targets and 35 Dn targets, and a nonredundant
        test set of 55 transmembrane proteins. It was shown that HSYMDOCK obtained
        a significantly better performance than other similar docking algorithms.
        The server supports both sequence and structure inputs for the monomer/subunit.
        Users have an option to provide the symmetry type of the complex, or the server
        can predict the symmetry type automatically. The docking process is fast and
        on average consumes 101/420 min for a docking job. The HSYMDOCK web server
        is available at http://huanglab.phys.hust.edu.cn/hsymdock/.
      authors:
      - name: Yan Y.
      - name: Tao H.
      - name: Huang S.-Y.
      citationCount: 33
      date: '2018-07-02T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'HSYMDOCK: A docking web server for predicting the structure of protein
        homo-oligomers with Cn or Dn symmetry'
    note: null
    pmcid: PMC6030965
    pmid: '29846641'
    type:
    - Primary
    version: null
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_2275
  validated: 1
  version:
  - '2018-06-02'
- accessibility: null
  additionDate: '2018-03-12T09:45:00Z'
  biotoolsCURIE: biotools:mobidb-lite
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  collectionID: []
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  credit:
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    fundrefid: null
    gridid: null
    name: University of Padua, Department of Biomedical Sciences, BioComputing UP
      lab
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: http://protein.bio.unipd.it/
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA-PADOVA
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
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    url: http://elixir.bio.unipd.it/
  - email: silvio.tosatto@unipd.it
    fundrefid: null
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    name: Silvio C.E. Tosatto
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: http://protein.bio.unipd.it
  description: MobiDB-lite is an optimized method for highly specific predictions
    of long intrinsically disordered regions
  documentation:
  - note: null
    type:
    - General
    url: http://protein.bio.unipd.it/mobidblite/
  download:
  - note: null
    type: Software package
    url: http://protein.bio.unipd.it/download/
    version: null
  editPermission:
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  function:
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    input:
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        term: Protein sequence
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      format:
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        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Protein feature detection
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    - term: Structure analysis
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    output:
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        term: Protein features
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      format:
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        uri: http://edamontology.org/format_3464
      - term: Sequence feature table format
        uri: http://edamontology.org/format_2548
  homepage: http://protein.bio.unipd.it/mobidblite/
  homepage_status: 0
  language:
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  lastUpdate: '2024-11-25T14:39:51.264257Z'
  license: CC-BY-NC-ND-4.0
  link: []
  maturity: Mature
  name: MobiDB-lite
  operatingSystem:
  - Linux
  otherID: []
  owner: ELIXIR-ITA-PADOVA
  publication:
  - doi: 10.1093/bioinformatics/btx015
    metadata:
      abstract: 'Motivation: Intrinsic disorder (ID) is established as an important
        feature of protein sequences. Its use in proteome annotation is however hampered
        by the availability of many methods with similar performance at the single
        residue level, which have mostly not been optimized to predict long ID regions
        of size comparable to domains. Results: Here, we have focused on providing
        a single consensus-based prediction, MobiDB-lite, optimized for highly specific
        (i.e. few false positive) predictions of long disorder. The method uses eight
        different predictors to derive a consensus which is then filtered for spurious
        short predictions. Consensus prediction is shown to outperform the single
        methods when annotating long ID regions. MobiDB-lite can be useful in large-scale
        annotation scenarios and has indeed already been integrated in the MobiDB,
        DisProt and InterPro databases.'
      authors:
      - name: Necci M.
      - name: Piovesan D.
      - name: Dosztanyi Z.
      - name: Tosatto S.C.E.
      citationCount: 139
      date: '2017-05-01T00:00:00Z'
      journal: Bioinformatics
      title: 'MobiDB-lite: Fast and highly specific consensus prediction of intrinsic
        disorder in proteins'
    note: null
    pmcid: null
    pmid: '28453683'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2018-06-04T16:46:37Z'
  biotoolsCURIE: biotools:rosettaes
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  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
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    fundrefid: null
    gridid: null
    name: Frank Dimaio
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: An automated tool that uses a fragment-based sampling strategy for
    de novo model completion of macromolecular structures from cryo-EM density maps
    at 3–5-Å resolution.
  documentation:
  - note: null
    type:
    - General
    url: https://media.nature.com/original/nature-assets/nmeth/journal/v14/n8/extref/nmeth.4340-S2.pdf
  download:
  - note: null
    type: API specification
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    version: null
  editPermission:
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    input:
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    - data:
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    note: null
    operation:
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  homepage: https://www.rosettacommons.org/
  homepage_status: 0
  language: []
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  license: Other
  link: []
  maturity: Mature
  name: RosettaES
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  - Windows
  - Mac
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  owner: ELIXIR-EE
  publication:
  - doi: 10.1038/nmeth.4340
    metadata:
      abstract: Accurate atomic modeling of macromolecular structures into cryo-electron
        microscopy (cryo-EM) maps is a major challenge, as the moderate resolution
        makes accurate placement of atoms difficult. We present Rosetta enumerative
        sampling (RosettaES), an automated tool that uses a fragment-based sampling
        strategy for de novo model completion of macromolecular structures from cryo-EM
        density maps at 3-5-Å resolution. On a benchmark set of nine proteins, RosettaES
        was able to identify near-native conformations in 85% of segments. RosettaES
        was also used to determine models for three challenging macromolecular structures.
      authors:
      - name: Frenz B.
      - name: Walls A.C.
      - name: Egelman E.H.
      - name: Veesler D.
      - name: Di Maio F.
      citationCount: 85
      date: '2017-07-28T00:00:00Z'
      journal: Nature Methods
      title: 'RosettaES: A sampling strategy enabling automated interpretation of
        difficult cryo-EMmaps'
    note: null
    pmcid: PMC6009829
    pmid: '28628127'
    type: []
    version: null
  relation: []
  toolType:
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  topic:
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  - term: Electron microscopy
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  - term: Structural biology
    uri: http://edamontology.org/topic_1317
  validated: 1
  version: []
- accessibility: null
  additionDate: '2018-07-11T10:55:58Z'
  biotoolsCURIE: biotools:unres
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  collectionID: []
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  cost: null
  credit:
  - email: cezary.czaplewski@ug.edu.pl
    fundrefid: null
    gridid: null
    name: Cezary Czaplewski
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: adam.liwo@ug.edu.pl
    fundrefid: null
    gridid: null
    name: Adam Liwo
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: A server implementation of the UNRES package for coarse-grained simulations
    of protein structures with the physics-based UNRES model. It can be used in simulations,
    including those aimed at protein-structure prediction, without ancillary information
    from structural databases; however, the implementation includes the possibility
    of using restraints. Local energy minimization, canonical molecular dynamics simulations,
    replica exchange and multiplexed replica exchange molecular dynamics simulations
    can be run
  documentation:
  - note: null
    type:
    - Training material
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  download: []
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  function:
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    input: []
    note: null
    operation:
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    output: []
  - cmd: null
    input:
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    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
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    note: null
    operation:
    - term: Ab initio structure prediction
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    output:
    - data:
        term: Protein structure report
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      format: []
  homepage: http://unres-server.chem.ug.edu.pl/
  homepage_status: 0
  language: []
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  license: null
  link: []
  maturity: null
  name: UNRES server
  operatingSystem: []
  otherID: []
  owner: aotamendi.1
  publication:
  - doi: 10.1093/nar/gky328
    metadata:
      abstract: A server implementation of the UNRES package (http://www.unres.pl)
        for coarse-grained simulations of protein structures with the physics-based
        UNRES model, coined a name UNRES server, is presented. In contrast to most
        of the protein coarsegrained models, owing to its physics-based origin, the
        UNRES force field can be used in simulations, including those aimed at protein-structure
        prediction, without ancillary information from structural databases; however,
        the implementation includes the possibility of using restraints. Local energy
        minimization, canonical molecular dynamics simulations, replica exchange and
        multiplexed replica exchange molecular dynamics simulations can be run with
        the current UNRES server; the latter are suitable for protein-structure prediction.
        The user-supplied input includes protein sequence and, optionally, restraints
        from secondary-structure prediction or small x-ray scattering data, and simulation
        type and parameters which are selected or typed in. Oligomeric proteins, as
        well as those containing D-amino-acid residues and disulfide links can be
        treated. The output is displayed graphically (minimized structures, trajectories,
        final models, analysis of trajectory/ensembles); however, all output files
        can be downloaded by the user.
      authors:
      - name: Czaplewski C.
      - name: Karczynska A.
      - name: Sieradzan A.K.
      - name: Liwo A.
      citationCount: 51
      date: '2018-07-02T00:00:00Z'
      journal: Nucleic Acids Research
      title: UNRES server for physics-based coarse-grained simulations and prediction
        of protein structure, dynamics and thermodynamics
    note: null
    pmcid: PMC6031057
    pmid: '29718313'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Molecular dynamics
    uri: http://edamontology.org/topic_0176
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  - term: NMR
    uri: http://edamontology.org/topic_0593
  validated: 1
  version: []
- accessibility: null
  additionDate: '2015-01-22T11:49:01Z'
  biotoolsCURIE: biotools:proabc
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    name: ELIXIR-ITA-SAPIENZA
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    typeEntity: Institute
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    url: null
  - email: pierpaolo.olimpieri@gmail.com
    fundrefid: null
    gridid: null
    name: Pier Paolo Olimpieri
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Predictor of Antibody-Antigen interactions based on the Random Forest
    Algorithm. User submitted sequences are automatically aligned and annotated according
    to their source organism and germline families.
  documentation:
  - note: null
    type:
    - General
    url: http://circe.med.uniroma1.it/proABC/help_proABC.php
  download: []
  editPermission:
    authors: []
    type: private
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    note: 'proABC estimates the residue-based probability for three different kind
      of interactions: Non-bonded Interactions, Hydrogen Bonds and Hydrophobic Interactions.'
    operation:
    - term: Protein interaction prediction
      uri: http://edamontology.org/operation_2492
    - term: Protein structure prediction
      uri: http://edamontology.org/operation_0474
    output:
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format: []
  homepage: http://www.biocomputing.it/proABC
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:26:05.307264Z'
  license: null
  link: []
  maturity: null
  name: proABC
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-ITA-SAPIENZA
  publication:
  - doi: 10.1093/bioinformatics/btt369
    metadata:
      abstract: 'Motivation: Antibodies or immunoglobulins are proteins of paramount
        importance in the immune system. They are extremely relevant as diagnostic,
        biotechnological and therapeutic tools. Their modular structure makes it easy
        to re-engineer them for specific purposes. Short of undergoing a trial and
        error process, these experiments, as well as others, need to rely on an understanding
        of the specific determinants of the antibody binding mode. Results: In this
        article, we present a method to identify, on the basis of the antibody sequence
        alone, which residues of an antibody directly interact with its cognate antigen.
        The method, based on the random forest automatic learning techniques, reaches
        a recall and specificity as high as 80% and is implemented as a free and easy-to-use
        server, named prediction of Antibody Contacts. We believe that it can be of
        great help in re-design experiments as well as a guide for molecular docking
        experiments. The results that we obtained also allowed us to dissect which
        features of the antibody sequence contribute most to the involvement of specific
        residues in binding to the antigen. © The Author 2013.'
      authors:
      - name: Olimpieri P.P.
      - name: Chailyan A.
      - name: Tramontano A.
      - name: Marcatili P.
      citationCount: 77
      date: '2013-09-15T00:00:00Z'
      journal: Bioinformatics
      title: 'Prediction of site-specific interactions in antibody-antigen complexes:
        The proABC method and server'
    note: null
    pmcid: PMC3753563
    pmid: '23803466'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2016-02-17T09:43:56Z'
  biotoolsCURIE: biotools:stitch
  biotoolsID: stitch
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
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    fundrefid: null
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    name: EMBL
    note: null
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    rorid: null
    typeEntity: Funding agency
    typeRole:
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    url: http://www.embl.org/
  - email: null
    fundrefid: null
    gridid: null
    name: SUND-KU
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: http://healthsciences.ku.dk/
  - email: null
    fundrefid: null
    gridid: null
    name: EC FP6
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: http://ec.europa.eu/research/index.cfm
  - email: null
    fundrefid: null
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    name: BMBF
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
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  - email: null
    fundrefid: null
    gridid: null
    name: EMBO
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: http://www.embo.org/
  - email: null
    fundrefid: null
    gridid: null
    name: CPR
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: http://www.cpr.ku.dk/
  - email: null
    fundrefid: null
    gridid: null
    name: TUD
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: http://www.biotec.tu-dresden.de/
  - email: null
    fundrefid: null
    gridid: null
    name: HD-HuB
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.hd-hub.de/
  - email: null
    fundrefid: null
    gridid: null
    name: Michael Kuhn
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: http://stitch1.embl.de/cgi/show_info_page.pl
  - email: null
    fundrefid: null
    gridid: null
    name: Michael Kuhn
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://stitch1.embl.de/cgi/show_info_page.pl
  description: Resource to explore known and predicted interactions of chemicals and
    proteins. Chemicals are linked to other chemicals and proteins by evidence derived
    from experiments, databases and the literature.
  documentation:
  - note: null
    type:
    - General
    url: http://stitch.embl.de/cgi/show_info_page.pl?UserId=pRfi11Qlkhnx&sessionId=sEfmbh_T7QLq
  download: []
  editPermission:
    authors:
    - larsjuhljensen
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Gene name
        uri: http://edamontology.org/data_2299
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: InChIKey
        uri: http://edamontology.org/format_1199
      - term: SMILES
        uri: http://edamontology.org/format_1196
      - term: xls
        uri: http://edamontology.org/format_3468
    - data:
        term: Protein name
        uri: http://edamontology.org/data_1009
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Compound name
        uri: http://edamontology.org/data_0990
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    note: STITCH is a database of protein – chemical interactions that integrates
      many sources of experimental and manually curated evidence with text-mining
      information and interaction predictions. Its key function is to provide users
      with predictions about the interactions that their entities of interest (proteins
      or small molecules) may be making with other such entities, and to visualise
      where a set of entities of interest can be found within the STITCH network.
      Direct traceable links to the original sources on which interactions are described
      in the network, make it easy for users to trace the provenance of the data.
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Pathway or network visualisation
      uri: http://edamontology.org/operation_3083
    - term: Pathway or network analysis
      uri: http://edamontology.org/operation_2497
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: Image format
        uri: http://edamontology.org/format_3547
    - data:
        term: Database cross-mapping
        uri: http://edamontology.org/data_0954
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Evidence
        uri: http://edamontology.org/data_2042
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://stitch.embl.de/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:25:13.779770Z'
  license: null
  link: []
  maturity: null
  name: STITCH
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: hdhub
  publication:
  - doi: 10.1093/nar/gkm795
    metadata:
      abstract: The knowledge about interactions between proteins and small molecules
        is essential for the understanding of molecular and cellular functions. However,
        information on such interactions is widely dispersed across numerous databases
        and the literature. To facilitate access to this data, STITCH ('search tool
        for interactions of chemicals') integrates information about interactions
        from metabolic pathways, crystal structures, binding experiments and drug-target
        relationships. Inferred information from phenotypic effects, text mining and
        chemical structure similarity is used to predict relations between chemicals.
        STITCH further allows exploring the network of chemical relations, also in
        the context of associated binding proteins. Each proposed interaction can
        be traced back to the original data sources. Our database contains interaction
        information for over 68 000 different chemicals, including 2200 drugs, and
        connects them to 1.5 million genes across 373 genomes and their interactions
        contained in the STRING database. STITCH is available at http://stitch.embl.de/.
        © 2007 The Author(s).
      authors:
      - name: Kuhn M.
      - name: von Mering C.
      - name: Campillos M.
      - name: Jensen L.J.
      - name: Bork P.
      citationCount: 754
      date: '2008-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'STITCH: Interaction networks of chemicals and proteins'
    note: null
    pmcid: PMC2238848
    pmid: '18084021'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkp937
    metadata:
      abstract: Over the last years, the publicly available knowledge on interactions
        between small molecules and proteins has been steadily increasing. To create
        a network of interactions, STITCH aims to integrate the data dispersed over
        the literature and various databases of biological pathways, drug-target relationships
        and binding affinities. In STITCH 2, the number of relevant interactions is
        increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics
        Database. The resulting network can be explored interactively or used as the
        basis for large-scale analyses. To facilitate links to other chemical databases,
        we adopt InChIKeys that allow identification of chemicals with a short, checksum-like
        string. STITCH 2.0 connects proteins from 630 organisms to over 74 000 different
        chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/.
        © The Author(s) 2009. Published by Oxford University Press.
      authors:
      - name: Kuhn M.
      - name: Szklarczyk D.
      - name: Franceschini A.
      - name: Campillos M.
      - name: Von Mering C.
      - name: Jensen L.J.
      - name: Beyer A.
      - name: Bork P.
      citationCount: 231
      date: '2009-11-06T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'STITCH 2: An interaction network database for small molecules and proteins'
    note: null
    pmcid: PMC2808890
    pmid: '19897548'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkt1207
    metadata:
      abstract: STITCH is a database of protein-chemical interactions that integrates
        many sources of experimental and manually curated evidence with text-mining
        information and interaction predictions. Available at http://stitch.embl.de,
        the resulting interaction network includes 390 000 chemicals and 3.6 million
        proteins from 1133 organisms. Compared with the previous version, the number
        of high-confidence protein-chemical interactions in human has increased by
        45%, to 367 000. In this version, we added features for users to upload their
        own data to STITCH in the form of internal identifiers, chemical structures
        or quantitative data. For example, a user can now upload a spreadsheet with
        screening hits to easily check which interactions are already known. To increase
        the coverage of STITCH, we expanded the text mining to include full-text articles
        and added a prediction method based on chemical structures. We further changed
        our scheme for transferring interactions between species to rely on orthology
        rather than protein similarity. This improves the performance within protein
        families, where scores are now transferred only to orthologous proteins, but
        not to paralogous proteins. STITCH can be accessed with a web-interface, an
        API and downloadable files. © 2013 The Author(s). Published by Oxford University
        Press.
      authors:
      - name: Kuhn M.
      - name: Szklarczyk D.
      - name: Pletscher-Frankild S.
      - name: Blicher T.H.
      - name: Von Mering C.
      - name: Jensen L.J.
      - name: Bork P.
      citationCount: 413
      date: '2014-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'STITCH 4: Integration of protein-chemical interactions with user data'
    note: null
    pmcid: PMC3964996
    pmid: '24293645'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkr1011
    metadata:
      abstract: To facilitate the study of interactions between proteins and chemicals,
        we have created STITCH, an aggregated database of interactions connecting
        over 300 000 chemicals and 2.6 million proteins from 1133 organisms. Compared
        to the previous version, the number of chemicals with interactions and the
        number of high-confidence interactions both increase 4-fold. The database
        can be accessed interactively through a web interface, displaying interactions
        in an integrated network view. It is also available for computational studies
        through downloadable files and an API. As an extension in the current version,
        we offer the option to switch between two levels of detail, namely whether
        stereoisomers of a given compound are shown as a merged entity or as separate
        entities. Separate display of stereoisomers is necessary, for example, for
        carbohydrates and chiral drugs. Combining the isomers increases the coverage,
        as interaction databases and publications found through text mining will often
        refer to compounds without specifying the stereoisomer. The database is accessible
        at http://stitch.embl.de/. © The Author(s) 2011.
      authors:
      - name: Kuhn M.
      - name: Szklarczyk D.
      - name: Franceschini A.
      - name: Von Mering C.
      - name: Jensen L.J.
      - name: Bork P.
      citationCount: 250
      date: '2012-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'STITCH 3: Zooming in on protein-chemical interactions'
    note: null
    pmcid: PMC3245073
    pmid: '22075997'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web application
  - Database portal
  topic:
  - term: Chemistry
    uri: http://edamontology.org/topic_3314
  - term: Biomedical science
    uri: http://edamontology.org/topic_3344
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 1
  version: []
- accessibility: null
  additionDate: '2018-03-12T09:31:50Z'
  biotoolsCURIE: biotools:soda-solubility
  biotoolsID: soda-solubility
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: University of Padua, Department of Biomedical Sciences, BioComputing UP
      lab
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: http://protein.bio.unipd.it/
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA-PADOVA
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: http://elixir.bio.unipd.it/
  - email: silvio.tosatto@unipd.it
    fundrefid: null
    gridid: null
    name: Silvio C.E. Tosatto
    note: null
    orcidid: http://orcid.org/0000-0003-4525-7793
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://protein.bio.unipd.it
  description: Protein SOlubility based on Disorder and Aggregation
  documentation:
  - note: null
    type:
    - General
    url: http://protein.bio.unipd.it/soda/help
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Protein secondary structure prediction
      uri: http://edamontology.org/operation_0267
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: http://protein.bio.unipd.it/soda/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-25T14:23:38.672551Z'
  license: CC-BY-NC-ND-4.0
  link: []
  maturity: Mature
  name: SODA
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-ITA-PADOVA
  publication:
  - doi: 10.1093/nar/gkx412
    metadata:
      abstract: Solubility is an important, albeit not well understood, feature determining
        protein behavior. It is of paramount importance in protein engineering, where
        similar folded proteins may behave in very different ways in solution. Here
        we present SODA, a novel method to predict the changes of protein solubility
        based on several physico-chemical properties of the protein. SODA uses the
        propensity of the protein sequence to aggregate as well as intrinsic disorder,
        plus hydrophobicity and secondary structure preferences to estimate changes
        in solubility. It has been trained and benchmarked on two different datasets.
        The comparison to other recently published methods shows that SODA has state-of-the-art
        performance and is particularly well suited to predict mutations decreasing
        solubility. The method is fast, returning results for single mutations in
        seconds. A usage example estimating the full repertoire of mutations for a
        human germline antibody highlights several solubility hotspots on the surface.
      authors:
      - name: Paladin L.
      - name: Piovesan D.
      - name: Tosatto S.C.E.
      citationCount: 47
      date: '2017-07-03T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'SODA: Prediction of protein solubility from disorder and aggregation
        propensity'
    note: null
    pmcid: PMC7059794
    pmid: '28505312'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web API
  - Web application
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Protein disordered structure
    uri: http://edamontology.org/topic_3538
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2018-07-18T09:31:39Z'
  biotoolsCURIE: biotools:raven_toolbox
  biotoolsID: raven_toolbox
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://gitter.im/SysBioChalmers/RAVEN?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
  - email: hao.wang@chalmers.se
    fundrefid: null
    gridid: null
    name: Hao Wang
    note: null
    orcidid: http://orcid.org/0000-0001-7475-0136
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: The RAVEN (Reconstruction, Analysis and Visualization of Metabolic
    Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated
    reconstruction of genome-scale models (GEMs). It makes use of published models
    and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality
    control features. The software suite also contains methods for visualizing simulation
    results and omics data, as well as a range of methods for performing simulations
    and analyzing the results. The software is a useful tool for system-wide data
    analysis in a metabolic context and for streamlined reconstruction of metabolic
    networks based on protein homology.
  documentation:
  - note: GitHub Wiki
    type:
    - General
    url: https://github.com/SysBioChalmers/RAVEN/wiki
  download:
  - note: Stabile releases
    type: Binaries
    url: https://github.com/SysBioChalmers/RAVEN/releases
    version: null
  - note: Source code
    type: Source code
    url: https://github.com/SysBioChalmers/RAVEN
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: protein
        uri: http://edamontology.org/format_1208
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: SBML
        uri: http://edamontology.org/format_2585
      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Pathway or network prediction
      uri: http://edamontology.org/operation_3439
    - term: Metabolic network modelling
      uri: http://edamontology.org/operation_3660
    - term: Pathway or network analysis
      uri: http://edamontology.org/operation_2497
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: SBML
        uri: http://edamontology.org/format_2585
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: YAML
        uri: http://edamontology.org/format_3750
    - data:
        term: Physiology parameter
        uri: http://edamontology.org/data_3722
      format:
      - term: raw
        uri: http://edamontology.org/format_1957
  homepage: https://github.com/SysBioChalmers/RAVEN
  homepage_status: 0
  language:
  - MATLAB
  lastUpdate: '2024-11-25T14:23:23.622737Z'
  license: GPL-3.0
  link:
  - note: Gitter chat room
    type:
    - Mailing list
    url: https://gitter.im/SysBioChalmers/RAVEN
  - note: GitHub Issues
    type:
    - Issue tracker
    url: https://github.com/SysBioChalmers/RAVEN/issues
  - note: GitHub Repository
    type:
    - Repository
    url: https://github.com/SysBioChalmers/RAVEN
  - note: GitHub Wiki
    type:
    - Helpdesk
    url: https://github.com/SysBioChalmers/RAVEN/wiki
  maturity: Mature
  name: RAVEN Toolbox
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: eduardk
  publication:
  - doi: 10.1101/321067
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  relation: []
  toolType:
  - Command-line tool
  - Script
  topic:
  - term: Computational biology
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  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Bioengineering
    uri: http://edamontology.org/topic_3398
  validated: 1
  version:
  - '2.0'
- accessibility: null
  additionDate: '2015-01-22T11:49:04Z'
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    url: null
  - email: paolo.marcatili@gmail.com
    fundrefid: null
    gridid: null
    name: Paolo Marcatili
    note: null
    orcidid: null
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    typeEntity: Person
    typeRole:
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    url: null
  description: Web server for the automatic modeling of immunoglobulin variable domains
    based on the canonical structure method. It has a user-friendly and flexible interface,
    that allows the user to choose templates (for the frameworks and the loops) and
    modeling strategies in an automatic or manual fashion.
  documentation:
  - note: null
    type:
    - General
    url: http://circe.med.uniroma1.it/pigs/help.php
  download: []
  editPermission:
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  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    note: Automatic prediction of immunoglobulin structures.
    operation:
    - term: Protein structure prediction
      uri: http://edamontology.org/operation_0474
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format: []
  homepage: http://circe.med.uniroma1.it/pigs/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:21:19.179245Z'
  license: null
  link: []
  maturity: null
  name: PIGS
  operatingSystem:
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  - Windows
  - Mac
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  owner: ELIXIR-ITA-SAPIENZA
  publication:
  - doi: 10.1038/nprot.2014.189
    metadata:
      abstract: Antibodies (or immunoglobulins) are crucial for defending organisms
        from pathogens, but they are also key players in many medical, diagnostic
        and biotechnological applications. The ability to predict their structure
        and the specific residues involved in antigen recognition has several useful
        applications in all of these areas. Over the years, we have developed or collaborated
        in developing a strategy that enables researchers to predict the 3D structure
        of antibodies with a very satisfactory accuracy. The strategy is completely
        automated and extremely fast, requiring only a few minutes (~10 min on average)
        to build a structural model of an antibody. It is based on the concept of
        canonical structures of antibody loops and on our understanding of the way
        light and heavy chains pack together.
      authors:
      - name: Marcatili P.
      - name: Olimpieri P.P.
      - name: Chailyan A.
      - name: Tramontano A.
      citationCount: 54
      date: '2014-11-20T00:00:00Z'
      journal: Nature Protocols
      title: Antibody structural modeling with prediction of immunoglobulin structure
        (PIGS)
    note: null
    pmcid: null
    pmid: '25375991'
    type:
    - Other
    version: null
  - doi: 10.1093/bioinformatics/btn341
    metadata:
      abstract: We describe a web server for the automatic prediction of immunoglobulin
        variable domains based on the canonical structure model. The server is user-friendly
        and flexible. It allows the user to select the templates for the frameworks
        and the loops using different strategies. The final output is a full-fledged
        3D model of the variable domains of the target immunoglobulin. © The Author
        2008. Published by Oxford University Press. All rights reserved.
      authors:
      - name: Marcatili P.
      - name: Rosi A.
      - name: Tramontano A.
      citationCount: 153
      date: '2008-09-01T00:00:00Z'
      journal: Bioinformatics
      title: 'PIGS: Automatic prediction of antibody structures'
    note: null
    pmcid: null
    pmid: '18641403'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2017-03-24T14:34:16Z'
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  biotoolsID: sib-blast
  collectionID:
  - BLAST utility
  confidence_flag: null
  cost: null
  credit:
  - email: bundschuh@mps.ohio-state.edu
    fundrefid: null
    gridid: null
    name: Ralf Bundschuh
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: SIB-BLAST is a web server for improved delineation of true and false
    positives in PSI-BLAST searches using the SimpleIsBeautiful (SIB) algorithm for
    sequence based homology detection.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioserv.mps.ohio-state.edu/sib-blast/Manual.html
  download: []
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  function:
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    input:
    - data:
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    note: null
    operation:
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    - term: Sequence alignment
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    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format: []
  homepage: http://bioserv.mps.ohio-state.edu/sib-blast/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:18:19.816961Z'
  license: null
  link: []
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  name: SIB-BLAST
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  - Mac
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  publication:
  - doi: 10.1093/nar/gkp301
    metadata:
      abstract: A SIB-BLAST web server (http://sib-blast.osc.edu) has been established
        for investigators to use the SimpleIsBeautiful (SIB) algorithm for sequence-based
        homology detection. SIB was developed to overcome the model corruption frequently
        observed in the later iterations of PSI-BLAST searches. The algorithm compares
        resultant hits from the second iteration to the final iteration of a PSI-BLAST
        search, calculates the figure of merit for each 'overlapped' hit and re-ranks
        the hits according to their figure of merit. By validating hits generated
        from the last profile against hits from the first profile when the model is
        least corrupted, the true and false positives are better delineated, which
        in turn, improves the accuracy of iterative PSI-BLAST searches. Notably, this
        improvement to PSI-BLAST comes at minimal computational cost as SIB-BLAST
        utilizes existing results already produced in a PSI-BLAST search.
      authors:
      - name: Lee M.M.
      - name: Chan M.K.
      - name: Bundschuh R.
      citationCount: 7
      date: '2009-08-04T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'SIB-BLAST: A web server for improved delineation of true and false positives
        in PSI-BLAST searches'
    note: null
    pmcid: PMC2703926
    pmid: '19429693'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Mathematics
    uri: http://edamontology.org/topic_3315
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-17T14:51:45Z'
  biotoolsCURIE: biotools:autohd
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  collectionID:
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  - Proteomics
  confidence_flag: null
  cost: null
  credit:
  - email: magnus.palmblad@gmail.com
    fundrefid: null
    gridid: null
    name: Magnus Palmblad
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  - email: webmaster@ms-utils.org
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Documentor
    url: http://ms-utils.org
  description: Analysis of H/D-exchange data using isotopic distributions.
  documentation:
  - note: null
    type:
    - General
    url: http://www.ms-utils.org/autohd.html
  download:
  - note: null
    type: Source code
    url: http://www.ms-utils.org/autohd_download.html
    version: null
  - note: null
    type: Source code
    url: http://www.ms-utils.org/autohd_download.html
    version: null
  editPermission:
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  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    note: null
    operation:
    - term: Protein hydrogen exchange rate calculation
      uri: http://edamontology.org/operation_0404
    output:
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://www.ms-utils.org/autohd.html
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-11-25T14:16:56.803274Z'
  license: GPL-3.0
  link:
  - note: null
    type:
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    url: http://ms-utils.org
  maturity: null
  name: AUTOHD
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: msutils_import
  publication:
  - doi: 10.1016/s1044-0305(01)00301-4
    metadata:
      abstract: High mass-resolving power has been shown to be useful for studying
        the conformational dynamics of proteins by hydrogen/deuterium (H/D) exchange.
        A computer algorithm was developed that automatically identifies peptides
        and their extent of deuterium incorporation from H/D exchange mass spectra
        of enzymatic digests or fragment ions produced by collisionally induced dissociation
        (CID) or electron capture dissociation (ECD). The computer algorithm compares
        measured and calculated isotopic distributions and uses a fast calculation
        of isotopic distributions using the fast Fourier transform (FFT). The algorithm
        facilitates rapid and automated analysis of H/D exchange mass spectra suitable
        for high-throughput approaches to the study of peptide and protein structures.
        The algorithm also makes the identification independent on comparisons with
        undeuterated control samples. The applicability of the algorithm was demonstrated
        on simulated isotopic distributions as well as on experimental data, such
        as Fourier transform ion cyclotron resonance (FTICR) mass spectra of myoglobin
        peptic digests, and CID and ECD spectra of substance P. Copyright © 2001 American
        Society for Mass Spectrometry.
      authors:
      - name: Palmblad M.
      - name: Buijs J.
      - name: Hakansson P.
      citationCount: 62
      date: '2001-12-01T00:00:00Z'
      journal: Journal of the American Society for Mass Spectrometry
      title: Automatic analysis of hydrogen/deuterium exchange mass spectra of peptides
        and proteins using calculations of isotopic distributions
    note: null
    pmcid: null
    pmid: '11720389'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-17T14:51:06Z'
  biotoolsCURIE: biotools:biolccc
  biotoolsID: biolccc
  collectionID:
  - ms-utils
  - Proteomics
  confidence_flag: null
  cost: null
  credit:
  - email: webmaster@ms-utils.org
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Documentor
    url: http://ms-utils.org
  description: An analytic model of peptide retention.
  documentation:
  - note: null
    type:
    - General
    url: http://theorchromo.ru/
  download:
  - note: null
    type: Source code
    url: http://packages.python.org/pyteomics.biolccc/API/mespaceBioLCCC.html
    version: null
  editPermission:
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  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: null
    operation:
    - term: Retention time prediction
      uri: http://edamontology.org/operation_3633
    output:
    - data:
        term: Peptide property
        uri: http://edamontology.org/data_2979
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: http://theorchromo.ru/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:16:48.686997Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://ms-utils.org
  maturity: null
  name: BioLCCC
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: msutils_import
  publication:
  - doi: 10.1021/ac060913x
    metadata:
      abstract: 'An approach to sequence-dependent retention time prediction of peptides
        based on the concept of liquid chromatography at critical conditions (LCCC)
        is presented. Within the LCCC approach applied to biopolymers (BioLCCC), the
        specific retention time corresponds to a particular sequence. In combination
        with mass spectrometry, this approach provides an efficient tool to solve
        problems wherein the protein sequencing is essential. In this work, we present
        a theoretical background of the BioLCCC concept and demonstrate experimentally
        its feasibility for sequence-dependent LC retention time prediction for peptides.
        BioLCCC model is based on three notions: (a) a random walk model for a macromolecule
        chain; (b) an entropy and energy compensation for the macromolecules within
        the adsorbent pore; and (c) a set of phenomenological parameters for the effective
        interaction energies of interactions between the amino acid residues and the
        adsorbent surface. In this work, the phenomenological parameters have been
        obtained for C18 reversed-phase HPLC. Note, that contrary to alternative additive
        models for retention time prediction based on summation of the so-called "retention
        coefficients", the BioLCCC approach takes into account the location of amino
        acids within the primary structure of a peptide and, thus, allows the identification
        of the peptides having the same composition of amino acids but differing by
        their arrangement. As a result, this new approach allows prediction of retention
        time for any possible amino acid sequence in particular HPLC experiments.
        In addition, the BioLCCC model lacks of main drawbacks of additive approaches
        that predict retention time for sequences of limited chain lengths and provide
        information about amino acid composition only. The proposed BioLCCC approach
        was characterized experimentally using LTQ FT LC-MS and LC-MS/MS data obtained
        earlier for Escherichia coli. The HPLC system calibration was performed using
        peptide retention standards. The results received show a linear correlation
        between predicted and experimental retention times, with a correlation coefficient,
        R2, of 0.97 for a peptide standard mixture and 0.9 for E. coli data, respectively,
        with the standard error below 1 min. The work presents the first description
        of a BioLCCC approach for high-throughput peptide characterization and preliminary
        results of its feasibility tests. © 2006 American Chemical Society.'
      authors:
      - name: Gorshkov A.V.
      - name: Tarasova I.A.
      - name: Evreinov V.V.
      - name: Savitski M.M.
      - name: Nielsen M.L.
      - name: Zubarev R.A.
      - name: Gorshkov M.V.
      citationCount: 71
      date: '2006-11-15T00:00:00Z'
      journal: Analytical Chemistry
      title: 'Liquid chromatography at critical conditions: Comprehensive approach
        to sequence-dependent retention time prediction'
    note: null
    pmcid: null
    pmid: '17105170'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-17T14:52:01Z'
  biotoolsCURIE: biotools:decoy.pl
  biotoolsID: decoy.pl
  collectionID:
  - ms-utils
  - Proteomics
  confidence_flag: null
  cost: null
  credit:
  - email: webmaster@ms-utils.org
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Documentor
    url: http://ms-utils.org
  description: Decoy database generator from Matrix Science.
  documentation:
  - note: null
    type:
    - General
    url: http://www.matrixscience.com/help/decoy_help.html#MANUAL
  download:
  - note: null
    type: Source code
    url: http://www.matrixscience.com/downloads/decoy.pl.gz
    version: null
  - note: null
    type: Source code
    url: http://www.matrixscience.com/downloads/decoy.pl.gz
    version: null
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    note: null
    operation:
    - term: Random sequence generation
      uri: http://edamontology.org/operation_0364
    output:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
  homepage: http://www.matrixscience.com/help/decoy_help.html
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2024-11-25T14:16:09.448059Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://ms-utils.org
  maturity: null
  name: decoy.pl
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: msutils_import
  publication:
  - doi: 10.1038/nmeth785
    metadata:
      abstract: Researchers have several options when designing proteomics experiments.
        Primary among these are choices of experimental method, instrumentation and
        spectral interpretation software. To evaluate these choices on a proteome
        scale, we compared triplicate measurements of the yeast proteome by liquid
        chromatography tandem mass spectrometry (LC-MS/MS) using linear ion trap (LTQ)
        and hybrid quadrupole time-of-flight (QqTOF; QSTAR) mass spectrometers. Acquired
        MS/MS spectra were interpreted with Mascot and SEQUEST algorithms with and
        without the requirement that all returned peptides be tryptic. Using a composite
        target decoy database strategy, we selected scoring criteria yielding 1% estimated
        false positive identifications at maximum sensitivity for all data sets, allowing
        reasonable comparisons between them. These comparisons indicate that Mascot
        and SEQUEST yield similar results for LTQ-acquired spectra but less so for
        QSTAR spectra. Furthermore, low reproducibility between replicate data acquisitions
        made on one or both instrument platforms can be exploited to increase sensitivity
        and confidence in large-scale protein identifications.
      authors:
      - name: Elias J.E.
      - name: Haas W.
      - name: Faherty B.K.
      - name: Gygi S.P.
      citationCount: 620
      date: '2005-09-01T00:00:00Z'
      journal: Nature Methods
      title: Comparative evaluation of mass spectrometry platforms used in large-scale
        proteomics investigations
    note: null
    pmcid: null
    pmid: '16118637'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-17T14:50:36Z'
  biotoolsCURIE: biotools:massxpert
  biotoolsID: massxpert
  collectionID:
  - ms-utils
  - Proteomics
  confidence_flag: null
  cost: null
  credit:
  - email: massxpert-maintainer@massxpert.org
    fundrefid: null
    gridid: null
    name: massXpert
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  - email: webmaster@ms-utils.org
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Documentor
    url: http://ms-utils.org
  description: Tool for analysis of polymer and peptide/protein mass spectra.
  documentation: []
  download:
  - note: null
    type: Source code
    url: http://download.tuxfamily.org/massxpert/source/
    version: null
  editPermission:
    authors:
    - ELIXIR-EE
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    type: group
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  function:
  - cmd: null
    input:
    - data:
        term: Tool identifier
        uri: http://edamontology.org/data_0977
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
    note: null
    operation:
    - term: Nucleic acid restriction digest
      uri: http://edamontology.org/operation_0365
    - term: Post-translation modification site prediction
      uri: http://edamontology.org/operation_0417
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    - term: Protein fragment weight comparison
      uri: http://edamontology.org/operation_2929
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Prediction and recognition (protein)
      uri: http://edamontology.org/operation_3023
    - term: Prediction and recognition (nucleic acid)
      uri: http://edamontology.org/operation_3024
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output:
    - data:
        term: Tool identifier
        uri: http://edamontology.org/data_0977
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
  homepage: http://www.massxpert.org
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:09:16.386925Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://ms-utils.org
  maturity: null
  name: massXpert
  operatingSystem: []
  otherID: []
  owner: rusconi
  publication:
  - doi: 10.1093/bioinformatics/btp504
    metadata:
      abstract: Since the middle of the 90s, mass spectrometry has evolved into an
        almost indispensable tool in structural studies on an ever-growing variety
        of (bio-)polymers, of which proteins, sugars and nucleic acids are the most
        prominent. Since the first public release of massXpert, the advances of mass
        spectrometry have motivated continuous and thorough maintenance of that software,
        in the form of two full software rewrites, culminating with massXpert 2, which
        we describe in this report. We shall describe the profound changes in massXpert
        that were performed so as to keep up with the technical advances in mass spectrometry
        since a decade. © The Author 2009. Published by Oxford University Press. All
        rights reserved.
      authors:
      - name: Rusconi F.
      citationCount: 16
      date: '2009-10-20T00:00:00Z'
      journal: Bioinformatics
      title: 'massXpert 2: A cross-platform software environment for polymer chemistry
        modelling and simulation/analysis of mass spectrometric data'
    note: null
    pmcid: null
    pmid: '19740912'
    type:
    - Primary
    version: null
  relation: []
  toolType:
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  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Nucleic acid sites, features and motifs
    uri: http://edamontology.org/topic_3511
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  - term: Protein modifications
    uri: http://edamontology.org/topic_0601
  validated: 1
  version:
  - massXpert 2
- accessibility: null
  additionDate: '2017-01-17T14:50:42Z'
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  collectionID:
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  - Proteomics
  confidence_flag: null
  cost: null
  credit:
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    fundrefid: null
    gridid: null
    name: Ulrich Omasits
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: webmaster@ms-utils.org
    fundrefid: null
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    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: http://ms-utils.org
  description: Interactive protein feature visualization and integration with experimental
    proteomic data.
  documentation:
  - note: null
    type:
    - General
    url: http://wlab.ethz.ch/protter/help/
  download:
  - note: null
    type: Source code
    url: http://ulo.github.io/Protter/
    version: null
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  - cmd: null
    input:
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      format:
      - term: protXML
        uri: http://edamontology.org/format_3747
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: uniprotkb-like format
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      - term: FASTA
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    - data:
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    note: null
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    - term: Topology diagram drawing
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    - term: GPCR prediction
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    - term: Protein feature detection
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    - term: MRM/SRM
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    output:
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      - term: SVG
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      - term: PDF
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  homepage: http://wlab.ethz.ch/protter/
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    metadata:
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        tool that supports interactive protein data analysis and hypothesis generation
        by visualizing both annotated sequence features and experimental proteomic
        data in the context of protein topology. Protter supports numerous proteomic
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        for large datasets. Visualizations of surfaceome datasets show the specific
        utility of Protter for the integrated visual analysis of membrane proteins
        and peptide selection for targeted proteomics. © 2013 The Author 2013. Published
        by Oxford University Press. All rights reserved.'
      authors:
      - name: Omasits U.
      - name: Ahrens C.H.
      - name: Muller S.
      - name: Wollscheid B.
      citationCount: 948
      date: '2014-03-01T00:00:00Z'
      journal: Bioinformatics
      title: 'Protter: Interactive protein feature visualization and integration with
        experimental proteomic data'
    note: null
    pmcid: null
    pmid: '24162465'
    type: []
    version: null
  relation: []
  toolType:
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  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  - term: Protein secondary structure
    uri: http://edamontology.org/topic_3542
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  validated: 1
  version: []
- accessibility: null
  additionDate: '2015-01-29T15:47:47Z'
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    name: Neil Rawlings
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    note: null
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  description: Search MEROPS sequences with BLAST.
  documentation:
  - note: null
    type:
    - Terms of use
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  - note: null
    type:
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    url: http://merops.sanger.ac.uk/about/special_features.shtml#BLAST
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      format: []
    note: The output includes protein similarity matches with active site residues
      annotated
    operation:
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    output:
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      format: []
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      format: []
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  name: MEROPS Blast
  operatingSystem:
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  owner: EMBL-EBI
  publication:
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        source of information about peptidases, their substrates and inhibitors, which
        are of great relevance to biology, medicine and biotechnology. The hierarchical
        classification of the database is as follows: homologous sets of sequences
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        along with the known substrate cleavages and peptidase-inhibitor interactions,
        and a link to the KEGG database of biological pathways. Links have also been
        established with the IUPHAR Guide to Pharmacology. A new service has been
        set up to allow the submission of identified substrate cleavages so that conservation
        of the cleavage site can be assessed. This should help establish whether or
        not a cleavage site is physiologically relevant on the basis that such a cleavage
        site is likely to be conserved.'
      authors:
      - name: Rawlings N.D.
      - name: Barrett A.J.
      - name: Finn R.
      citationCount: 558
      date: '2016-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: Twenty years of the MEROPS database of proteolytic enzymes, their substrates
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    note: null
    pmcid: PMC4702814
    pmid: '26527717'
    type:
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    version: null
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  topic:
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  validated: 1
  version:
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  description: BLAST search against Kinase domains stored in Kinase SARfari.
  documentation:
  - note: null
    type:
    - Terms of use
    url: http://www.ebi.ac.uk/about/terms-of-use
  - note: null
    type:
    - General
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    input:
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    note: null
    operation:
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    output:
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      format: []
  homepage: https://www.ebi.ac.uk/chembl/sarfari/kinasesarfari/protein
  homepage_status: 0
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  name: Kinase SARfari  BLAST Search
  operatingSystem:
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  otherID: []
  owner: EMBL-EBI
  publication:
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    metadata:
      abstract: 'ChEMBL is an Open Data database containing binding, functional and
        ADMET information for a large number of drug-like bioactive compounds. These
        data are manually abstracted from the primary published literature on a regular
        basis, then further curated and standardized to maximize their quality and
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        problems. Currently, the database contains 5.4 million bioactivity measurements
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        chembldb. © The Author(s) 2011. Published by Oxford University Press.'
      authors:
      - name: Gaulton A.
      - name: Bellis L.J.
      - name: Bento A.P.
      - name: Chambers J.
      - name: Davies M.
      - name: Hersey A.
      - name: Light Y.
      - name: McGlinchey S.
      - name: Michalovich D.
      - name: Al-Lazikani B.
      - name: Overington J.P.
      citationCount: 3079
      date: '2012-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'ChEMBL: A large-scale bioactivity database for drug discovery'
    note: null
    pmcid: PMC3245175
    pmid: '21948594'
    type:
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  topic:
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  validated: 0
  version:
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  additionDate: '2015-01-29T15:44:14Z'
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  description: BLAST search against protein targets stored in Malaria Data database.
  documentation:
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    - Terms of use
    url: http://www.ebi.ac.uk/about/terms-of-use
  - note: null
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    metadata:
      abstract: 'ChEMBL is an Open Data database containing binding, functional and
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        data are manually abstracted from the primary published literature on a regular
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        utility across a wide range of chemical biology and drug-discovery research
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        chembldb. © The Author(s) 2011. Published by Oxford University Press.'
      authors:
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      - name: Bellis L.J.
      - name: Bento A.P.
      - name: Chambers J.
      - name: Davies M.
      - name: Hersey A.
      - name: Light Y.
      - name: McGlinchey S.
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      title: 'ChEMBL: A large-scale bioactivity database for drug discovery'
    note: null
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  validated: 0
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  description: Search UniProt sequences with BLAST.
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    output:
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  homepage: http://www.uniprot.org/blast/
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  owner: EMBL-EBI
  publication:
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    metadata:
      abstract: UniProt is an important collection of protein sequences and their
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        past year. This growth in sequences has prompted an extension of UniProt accession
        number space from 6 to 10 characters. An increasing fraction of new sequences
        are identical to a sequence that already exists in the database with the majority
        of sequences coming from genome sequencing projects. We have created a new
        proteome identifier that uniquely identifies a particular assembly of a species
        and strain or subspecies to help users track the provenance of sequences.
        We present a new website that has been designed using a user-experience design
        process. We have introduced an annotation score for all entries in UniProt
        to represent the relative amount of knowledge known about each protein. These
        scores will be helpful in identifying which proteins are the best characterized
        and most informative for comparative analysis. All UniProt data is provided
        freely and is available on the web at http://www.uniprot.org/.
      authors:
      - name: Bateman A.
      - name: Martin M.J.
      - name: O'Donovan C.
      - name: Magrane M.
      - name: Apweiler R.
      - name: Alpi E.
      - name: Antunes R.
      - name: Arganiska J.
      - name: Bely B.
      - name: Bingley M.
      - name: Bonilla C.
      - name: Britto R.
      - name: Bursteinas B.
      - name: Chavali G.
      - name: Cibrian-Uhalte E.
      - name: Da Silva A.
      - name: De Giorgi M.
      - name: Dogan T.
      - name: Fazzini F.
      - name: Gane P.
      - name: Castro L.G.
      - name: Garmiri P.
      - name: Hatton-Ellis E.
      - name: Hieta R.
      - name: Huntley R.
      - name: Legge D.
      - name: Liu W.
      - name: Luo J.
      - name: Macdougall A.
      - name: Mutowo P.
      - name: Nightingale A.
      - name: Orchard S.
      - name: Pichler K.
      - name: Poggioli D.
      - name: Pundir S.
      - name: Pureza L.
      - name: Qi G.
      - name: Rosanoff S.
      - name: Saidi R.
      - name: Sawford T.
      - name: Shypitsyna A.
      - name: Turner E.
      - name: Volynkin V.
      - name: Wardell T.
      - name: Watkins X.
      - name: Zellner H.
      - name: Cowley A.
      - name: Figueira L.
      - name: Li W.
      - name: McWilliam H.
      - name: Lopez R.
      - name: Xenarios I.
      - name: Bougueleret L.
      - name: Bridge A.
      - name: Poux S.
      - name: Redaschi N.
      - name: Aimo L.
      - name: Argoud-Puy G.
      - name: Auchincloss A.
      - name: Axelsen K.
      - name: Bansal P.
      - name: Baratin D.
      - name: Blatter M.-C.
      - name: Boeckmann B.
      - name: Bolleman J.
      - name: Boutet E.
      - name: Breuza L.
      - name: Casal-Casas C.
      - name: De Castro E.
      - name: Coudert E.
      - name: Cuche B.
      - name: Doche M.
      - name: Dornevil D.
      - name: Duvaud S.
      - name: Estreicher A.
      - name: Famiglietti L.
      - name: Feuermann M.
      - name: Gasteiger E.
      - name: Gehant S.
      - name: Gerritsen V.
      - name: Gos A.
      - name: Gruaz-Gumowski N.
      - name: Hinz U.
      - name: Hulo C.
      - name: Jungo F.
      - name: Keller G.
      - name: Lara V.
      - name: Lemercier P.
      - name: Lieberherr D.
      - name: Lombardot T.
      - name: Martin X.
      - name: Masson P.
      - name: Morgat A.
      - name: Neto T.
      - name: Nouspikel N.
      - name: Paesano S.
      - name: Pedruzzi I.
      - name: Pilbout S.
      - name: Pozzato M.
      - name: Pruess M.
      - name: Rivoire C.
      - name: Roechert B.
      - name: Schneider M.
      - name: Sigrist C.
      - name: Sonesson K.
      - name: Staehli S.
      - name: Stutz A.
      - name: Sundaram S.
      - name: Tognolli M.
      - name: Verbregue L.
      - name: Veuthey A.L.
      - name: Wu C.H.
      - name: Arighi C.N.
      - name: Arminski L.
      - name: Chen C.
      - name: Chen Y.
      - name: Garavelli J.S.
      - name: Huang H.
      - name: Laiho K.
      - name: McGarvey P.
      - name: Natale D.A.
      - name: Suzek B.E.
      - name: Vinayaka C.R.
      - name: Wang Q.
      - name: Wang Y.
      - name: Yeh L.-S.
      - name: Yerramalla M.S.
      - name: Zhang J.
      citationCount: 3931
      date: '2015-01-28T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'UniProt: A hub for protein information'
    note: null
    pmcid: PMC4384041
    pmid: '25348405'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: blast
    type: uses
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2015-01-29T15:44:07Z'
  biotoolsCURIE: biotools:gpcr_sarfari_blast_search
  biotoolsID: gpcr_sarfari_blast_search
  collectionID:
  - BLAST
  - ChEMBL Tools
  - EBI Tools
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: ChEMBL Team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: EMBL-EBI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: chembl-help@ebi.ac.uk
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: mdavies@ebi.ac.uk
    fundrefid: null
    gridid: null
    name: Mark Davies
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: BLAST search of against GPCR domains stored in GPCR SARfari.
  documentation:
  - note: null
    type:
    - Terms of use
    url: http://www.ebi.ac.uk/about/terms-of-use
  - note: null
    type:
    - General
    url: https://www.ebi.ac.uk/chembl/sarfari/gpcrsarfari/protein
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format: []
  homepage: https://www.ebi.ac.uk/chembl/sarfari/gpcrsarfari/protein
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:07:22.092242Z'
  license: null
  link: []
  maturity: null
  name: GPCR SARfari  BLAST Search
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: EMBL-EBI
  publication:
  - doi: 10.1093/bioinformatics/btv010
    metadata:
      abstract: 'Motivation: ADME SARfari is a freely available web resource that
        enables comparative analyses of drug-disposition genes. It does so by integrating
        a number of publicly available data sources, which have subsequently been
        used to build data mining services, predictive tools and visualizations for
        drug metabolism researchers. The data include the interactions of small molecules
        with ADME (absorption, distribution, metabolism and excretion) proteins responsible
        for the metabolism and transport of molecules; available pharmacokinetic (PK)
        data; protein sequences of ADME-related molecular targets for pre-clinical
        model species and human; alignments of the orthologues including information
        on known SNPs (Single Nucleotide Polymorphism) and information on the tissue
        distribution of these proteins. In addition, in silico models have been developed,
        which enable users to predict which ADME relevant protein targets a novel
        compound is likely to interact with.'
      authors:
      - name: Davies M.
      - name: Dedman N.
      - name: Hersey A.
      - name: Papadatos G.
      - name: Hall M.D.
      - name: Cucurull-Sanchez L.
      - name: Jeffrey P.
      - name: Hasan S.
      - name: Eddershaw P.J.
      - name: Overington J.P.
      citationCount: 15
      date: '2015-05-15T00:00:00Z'
      journal: Bioinformatics
      title: 'ADME SARfari: Comparative genomics of drug metabolizing systems'
    note: null
    pmcid: PMC4426839
    pmid: '25964657'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: blast
    type: uses
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Membrane and lipoproteins
    uri: http://edamontology.org/topic_0820
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  validated: 0
  version:
  - '1'
next: ?page=2
previous: null
