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        uri: http://edamontology.org/data_0896
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://busca.biocomp.unibo.it/deepsig/
  homepage_status: 0
  language:
  - Python
  - C++
  lastUpdate: '2025-06-19T11:55:09.017105Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: DeepSig
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-ITA-BOLOGNA
  publication:
  - doi: 10.1093/bioinformatics/btx818
    metadata:
      abstract: Motivation The identification of signal peptides in protein sequences
        is an important step toward protein localization and function characterization.
        Results Here, we present DeepSig, an improved approach for signal peptide
        detection and cleavage-site prediction based on deep learning methods. Comparative
        benchmarks performed on an updated independent dataset of proteins show that
        DeepSig is the current best performing method, scoring better than other available
        state-of-the-art approaches on both signal peptide detection and precise cleavage-site
        identification. Availability and implementation DeepSig is available as both
        standalone program and web server at https://deepsig.biocomp.unibo.it. All
        datasets used in this study can be obtained from the same website.
      authors:
      - name: Savojardo C.
      - name: Martelli P.L.
      - name: Fariselli P.
      - name: Casadio R.
      citationCount: 96
      date: '2018-05-15T00:00:00Z'
      journal: Bioinformatics
      title: 'DeepSig: Deep learning improves signal peptide detection in proteins'
    note: null
    pmcid: PMC5946842
    pmid: '29280997'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  validated: 1
  version:
  - 1.2.5
- accessibility: null
  additionDate: '2015-06-29T10:14:28Z'
  biotoolsCURIE: biotools:netpicorna
  biotoolsID: netpicorna
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: CBS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: nikob@cbs.dtu.dk
    fundrefid: null
    gridid: null
    name: Nikolaj Sorgenfrei Blom
    note: null
    orcidid: https://orcid.org/0000-0001-7787-7853
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Neural network predictions of cleavage sites of picornaviral proteases.
  documentation:
  - note: null
    type:
    - General
    url: http://www.cbs.dtu.dk/services/NetPicoRNA/instructions.php
  download: []
  editPermission:
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    - powehi
    type: group
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: produces neural network predictions of cleavage sites of picornaviral proteases
    operation:
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
  homepage: http://cbs.dtu.dk/services/NetPicoRNA/
  homepage_status: 0
  language: []
  lastUpdate: '2025-04-21T12:49:56.070719Z'
  license: Other
  link:
  - note: null
    type:
    - Software catalogue
    url: http://cbs.dtu.dk/services
  maturity: Legacy
  name: NetPicoRNA
  operatingSystem:
  - Linux
  otherID: []
  owner: powehi
  publication:
  - doi: 10.1002/pro.5560051107
    metadata:
      abstract: Picornaviral proteinases are responsible for maturation cleavages
        of the viral polyprotein, but also catalyze the degradation of cellular targets.
        Using graphical visualization techniques and neural network algorithms, we
        have investigated the sequence specificity of the two proteinases 2A(pro)
        and 3C(pro). The cleavage of VP0 (giving rise to VP2 and VP4), which is carried
        out by a so-far unknown proteinase, was also examined. In combination with
        a novel surface exposure prediction algorithm, our neural network approach
        successfully distinguishes known cleavage sites from noncleavage sites and
        yields a more consistent definition of features common to these sites. The
        method is able to predict experimentally determined cleavage sites in cellular
        proteins. We present a list of mammalian and other proteins that are predicted
        to be possible targets for the vital proteinases. Whether these proteins are
        indeed cleaved awaits experimental verification. Additionally, we report several
        errors detected in the protein databases.
      authors:
      - name: Blom N.
      - name: Hansen J.
      - name: Blaas D.
      - name: Brunak S.
      citationCount: 204
      date: '1996-01-01T00:00:00Z'
      journal: Protein Science
      title: 'Cleavage site analysis in picornaviral polyproteins: Discovering cellular
        targets by neural networks'
    note: null
    pmcid: PMC2143287
    pmid: '8931139'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2020-11-09T21:38:53Z'
  biotoolsCURIE: biotools:trend_protein_evolution_function
  biotoolsID: trend_protein_evolution_function
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: gumerov.1@osu.edu
    fundrefid: null
    gridid: null
    name: Vadim Gumerov
    note: null
    orcidid: https://orcid.org/0000-0003-1670-7679
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: TREND is a platform that allows researchers to explore protein function
    and evolution identifying protein features, gene neighborhoods and operons, clustering
    neighboring genes, and integrating all these data into phylogenomic context and
    cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides
    ample opportunities for adjusting each step of the analysis.
  documentation:
  - note: null
    type:
    - User manual
    url: http://trend.evobionet.com/help
  download: []
  editPermission:
    authors: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence alignment
        uri: http://edamontology.org/data_1384
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence set (protein)
        uri: http://edamontology.org/data_1233
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: NCBI locus tag
        uri: http://edamontology.org/data_1900
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: RefSeq accession (protein)
        uri: http://edamontology.org/data_2385
      format: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Phylogenetic inference
      uri: http://edamontology.org/operation_0323
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    - term: Sequence classification
      uri: http://edamontology.org/operation_2995
    - term: Protein domain recognition
      uri: http://edamontology.org/operation_0246
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    output:
    - data:
        term: Protein sequence alignment
        uri: http://edamontology.org/data_1384
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Sequence cluster (protein)
        uri: http://edamontology.org/data_1245
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: http://trend.evobionet.com/
  homepage_status: 0
  language: []
  lastUpdate: '2024-12-17T20:42:49.942166Z'
  license: null
  link: []
  maturity: null
  name: TREND Protein Evolution Function
  operatingSystem: []
  otherID: []
  owner: vadim
  publication:
  - doi: 10.1093/nar/gkaa243
    metadata:
      abstract: Key steps in a computational study of protein function involve analysis
        of (i) relationships between homologous proteins, (ii) protein domain architecture
        and (iii) gene neighborhoods the corresponding proteins are encoded in. Each
        of these steps requires a separate computational task and sets of tools. Currently
        in order to relate protein features and gene neighborhoods information to
        phylogeny, researchers need to prepare all the necessary data and combine
        them by hand, which is time-consuming and error-prone. Here, we present a
        new platform, TREND (tree-based exploration of neighborhoods and domains),
        which can perform all the necessary steps in automated fashion and put the
        derived information into phylogenomic context, thus making evolutionary based
        protein function analysis more efficient. A rich set of adjustable components
        allows a user to run the computational steps specific to his task. TREND is
        freely available at http://trend.zhulinlab.org.
      authors:
      - name: Gumerov V.M.
      - name: Zhulin I.B.
      citationCount: 33
      date: '2021-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'TREND: a platform for exploring protein function in prokaryotes based
        on phylogenetic, domain architecture and gene neighborhood analyses'
    note: null
    pmcid: PMC7319448
    pmid: '32282909'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkac034
    metadata:
      abstract: TheURL address of the web server published in this article has been
        changed fromhttp://trend.zhulinlab.org to http://trend. evobionet.com/.
      authors:
      - name: Gumerov V.M.
      - name: Zhulin I.B.
      citationCount: 6
      date: '2022-02-22T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'Erratum: TREND: A platform for exploring protein function in prokaryotes
        based on phylogenetic, domain architecture and gene neighborhood analyses
        (Nucleic Acids Research DOI: 10.1093/nar/gkaa243)'
    note: 'Can be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937'
    pmcid: PMC8860576
    pmid: '35100406'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: null
  additionDate: '2015-08-24T10:00:36Z'
  biotoolsCURIE: biotools:cofactory
  biotoolsID: cofactory
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: CBS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: tnp@cbs.dtu.dk
    fundrefid: null
    gridid: null
    name: Thomas Nordahl Petersen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Identification of Rossmann folds and prediction of FAD, NAD and NADP
    specificity.
  documentation:
  - note: null
    type:
    - General
    url: http://www.cbs.dtu.dk/services/Cofactory/instructions.php
  download:
  - note: null
    type: Source code
    url: http://www.cbs.dtu.dk/services/doc/cofactory-1.0.readme
    version: null
  - note: null
    type: Binaries
    url: http://www.cbs.dtu.dk/services/doc/cofactory-1.0.readme
    version: null
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: identifies Rossmann fold sequence domains and predicts their specificity
      for the cofactors FAD, NAD or NADP
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://cbs.dtu.dk/services/Cofactory/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:22:09.216410Z'
  license: Other
  link:
  - note: null
    type:
    - Repository
    url: http://www.cbs.dtu.dk/services/doc/cofactory-1.0.readme
  - note: null
    type:
    - Software catalogue
    url: http://cbs.dtu.dk/services
  maturity: Emerging
  name: Cofactory
  operatingSystem:
  - Linux
  otherID: []
  owner: CBS
  publication:
  - doi: 10.1002/prot.24536
    metadata: null
    note: null
    pmcid: null
    pmid: '24523134'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  validated: 1
  version:
  - '2.1'
- accessibility: null
  additionDate: '2017-02-10T11:35:59Z'
  biotoolsCURIE: biotools:ibm_pattern_discovery
  biotoolsID: ibm_pattern_discovery
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Extensive server possessing a wide range of tools for pattern discovery
    in DNA and protein sequences as well as in text. Tools for multiple sequence alignment,
    gene discovery, protein annotation, and other applications also exist on this
    server. A detailed help page is provided for all tools.
  documentation: []
  download: []
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  function:
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    input: []
    note: null
    operation:
    - term: Indel detection
      uri: http://edamontology.org/operation_0452
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Protein sequence analysis
      uri: http://edamontology.org/operation_2479
    - term: Service discovery
      uri: http://edamontology.org/operation_3761
    - term: Sequence motif discovery
      uri: http://edamontology.org/operation_0238
    output: []
  homepage: http://cbcsrv.watson.ibm.com/Tspd.html
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:21:22.845224Z'
  license: null
  link: []
  maturity: null
  name: IBM Bioinformatics and Pattern Discovery Group
  operatingSystem: []
  otherID: []
  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/nar/gkf338
    metadata: null
    note: null
    pmcid: PMC117281
    pmid: '12060689'
    type: []
    version: null
  - doi: 10.1093/bioinformatics/14.1.55
    metadata: null
    note: null
    pmcid: null
    pmid: '9520502'
    type: []
    version: null
  - doi: 10.1093/nar/gkg621
    metadata: null
    note: null
    pmcid: PMC169027
    pmid: '12824385'
    type: []
    version: null
  - doi: 10.1093/nar/gkf464
    metadata: null
    note: null
    pmcid: PMC137405
    pmid: '12202776'
    type: []
    version: null
  - doi: 10.1006/mben.2000.0151
    metadata: null
    note: null
    pmcid: null
    pmid: '11056059'
    type: []
    version: null
  - doi: 10.1093/nar/gkh367
    metadata: null
    note: null
    pmcid: PMC441505
    pmid: '15215340'
    type: []
    version: null
  - doi: null
    metadata: null
    note: null
    pmcid: null
    pmid: '10786305'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-02-10T11:35:35Z'
  biotoolsCURIE: biotools:repper
  biotoolsID: repper
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Tool for detecting and analysing regions in protein sequences or sequence
    alignements that have short gapless repeats.
  documentation: []
  download: []
  editPermission:
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    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Repeat sequence detection
      uri: http://edamontology.org/operation_0379
    - term: Protein sequence analysis
      uri: http://edamontology.org/operation_2479
    - term: Repeat sequence organisation analysis
      uri: http://edamontology.org/operation_0380
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    output: []
  homepage: http://protevo.eb.tuebingen.mpg.de/repper
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:21:15.799334Z'
  license: null
  link: []
  maturity: null
  name: REPPER
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  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/nar/gki405
    metadata: null
    note: null
    pmcid: PMC1160166
    pmid: '15980460'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-02-10T11:34:11Z'
  biotoolsCURIE: biotools:grabcas
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  description: Tool for predicting granzyme B and caspase cleavage sites.
  documentation: []
  download: []
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Splice site prediction
      uri: http://edamontology.org/operation_0433
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    - term: Protein binding site prediction
      uri: http://edamontology.org/operation_2575
    output: []
  homepage: http://www.uniklinikum-saarland.de/einrichtungen/fachrichtungen/humangenetik/software/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:20:37.094515Z'
  license: null
  link: []
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  name: GraBCas
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  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/nar/gki433
    metadata: null
    note: null
    pmcid: PMC1160194
    pmid: '15980455'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-03-25T17:08:06Z'
  biotoolsCURIE: biotools:plantloc
  biotoolsID: plantloc
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Web server for predicting plant protein subcellular localization by
    substantiality motif.
  documentation: []
  download: []
  editPermission:
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    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Protein subcellular localisation prediction
      uri: http://edamontology.org/operation_2489
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    - term: Protein function prediction
      uri: http://edamontology.org/operation_1777
    output: []
  homepage: http://cal.tongji.edu.cn/PlantLoc/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:20:12.870509Z'
  license: null
  link: []
  maturity: null
  name: PlantLoc
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  otherID: []
  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/nar/gkt428
    metadata: null
    note: null
    pmcid: PMC3692052
    pmid: '23729470'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Plants
    uri: http://edamontology.org/topic_0780
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  description: This server is able to calculate the atom depth value for every atom
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  description: The tool finds the Knobs-into-Holes mode of packing between alpha-helices
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  toolType:
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  toolType:
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  - term: Protein structural motifs and surfaces
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  description: Database that contains information on functional site amino acid positions
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    using superimpositions.
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  description: This uses a graph-based model to describe the structure of proteins
    on the super-secondary structure level. A protein-ligand graph is computed from
    the atomic coordinates in a PDB file and the secondary structure assignments of
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  biotoolsCURIE: biotools:aquaria
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  description: Simplifying the generation of insight from protein structures through
    structure visualisation, annotated with protein features; loads sequence-to-structure
    alignments from the PSSH2 database, sequence features from UniProt and Interpro
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  download:
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    type: Binaries
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  function:
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    input:
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    - data:
        term: Organism identifier
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      format:
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    note: You can find sequences based on a keyword search. For the identified sequence,
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      between sequence and structure). accession number, ID or part of the name or
      alias from UniProt Organism names used in UniProt; Homo sapiens used by default
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    - term: Sequence database search
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    output: []
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    input:
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    note: 'web service to get matching structures with alignment data for a given
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      format:
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        uri: http://edamontology.org/format_3464
  homepage: http://aquaria.ws
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  language:
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  lastUpdate: '2024-11-25T15:45:50.420021Z'
  license: GPL-2.0
  link:
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    type:
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  maturity: Mature
  name: Aquaria
  operatingSystem:
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  otherID: []
  owner: RostLab
  publication:
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    metadata: null
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  relation: []
  toolType:
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  topic:
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  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  validated: 1
  version:
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next: ?page=2
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