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      The InterPro protein families database: the classification resource after 15 years

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      1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 2 , 3 , 3 , 3 , 3 , 4 , 5 , 6 , 6 , 7 , 7 , 8 , 8 , 9 , 10 , 10 , 10 , 11 , 12 , 12 , 13 , 13 , 1 , *
      Nucleic Acids Research
      Oxford University Press

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          Abstract

          The InterPro database ( http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36 766 member database signatures integrated into 26 238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012.

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          Most cited references15

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Activities at the Universal Protein Resource (UniProt)

            The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation. It integrates, interprets and standardizes data from literature and numerous resources to achieve the most comprehensive catalog possible of protein information. The central activities are the biocuration of the UniProt Knowledgebase and the dissemination of these data through our Web site and web services. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.
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              The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

              The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                28 January 2015
                26 November 2014
                26 November 2014
                : 43
                : Database issue , Database issue
                : D213-D221
                Affiliations
                [1 ]European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
                [2 ]Faculty of Life Science and School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
                [3 ]Swiss Institute of Bioinformatics (SIB), CMU - Rue Michel-Servet, 1211 Geneva 4, Switzerland
                [4 ]Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
                [5 ]Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
                [6 ]Pôle Rhône-Alpin de Bio-Informatique (PRABI), Batiment G. Mendel, Universite Claude Bernard, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
                [7 ]European Molecular Laboratory (EMBL), Meyerhofstasse 1, 69117 Heidelberg, Germany
                [8 ]Department of Computer Science, University of Bristol, Woodland Road, Bristol, BS8 1UB, UK
                [9 ]J. Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, MD 20850, USA
                [10 ]Protein Information Resource (PIR), Georgetown University Medical Center, Washington, DC 20007, USA
                [11 ]Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
                [12 ]Structural and Molecular Biology Department, University College London, University of London, London, WC1E 6BT, UK
                [13 ]Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
                Author notes
                [* ]To whom correspondence should be addressed. Tel: +44 1223 494 481; Fax: +44 1223 494 468; Email: rdf@ 123456ebi.ac.uk
                Author information
                http://orcid.org/0000-0003-3560-4288
                Article
                10.1093/nar/gku1243
                4383996
                25428371
                e13e8362-015c-4415-81c3-d63ee2378a53
                © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 11 November 2014
                : 10 November 2014
                : 20 October 2014
                Page count
                Pages: 9
                Categories
                Database Issue
                Custom metadata
                28 January 2015

                Genetics
                Genetics

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