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      InterPro in 2011: new developments in the family and domain prediction database

      research-article
      Author(s): 1 , * , 1 , * , 1 , * , 1 , 2 , 3 , 4 , 1 , 5 , 1 , 6 , 3 , 1 , 1 , 1 , 4 , 3 , 1 , 7 , 8 , 6 , 4 , 9 , 5 , 1 , 1 , 7 , 1 , 1 , 1 , 1 , 10 , 1 , 9 , 11 , 12 , 1 , 3 , 1 , 6 , 1 , 8 , 6 , 1 , 3 , 1 , 10 , 12 , 12 , 1
      Publication date (Electronic):
      Journal: Nucleic Acids Research
      Publisher: Oxford University Press

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          Abstract

          InterPro ( http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          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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            The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

            Helen Berman, Kim Henrick, Haruki Nakamura … (2006)
            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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              The ENZYME database in 2000.

              A Bairoch (2000)
              The ENZYME database is a repository of information related to the nomenclature of enzymes. In recent years it has became an indispensable resource for the development of metabolic databases. The current version contains information on 3705 enzymes. It is available through the ExPASy WWW server (http://www.expasy.ch/enzyme/ ).
              Article 0 comments Cited 356 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: January 2012
                Publication date (Print): January 2012
                Publication date (Electronic): 16 November 2011
                Publication date PMC-release: 16 November 2011
                Volume: 40
                Issue: D1 , Database issue
                Pages: D306-D312
                Affiliations
                1EMBL Outstation European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, 2Faculty of Life Science and School of Computer Science, The University of Manchester, M13 9PL, Manchester, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK, 4Pôle Rhône-Alpin de Bio-Informatique (PRABI) and Laboratoire de Biométrie et Biologie Evolutive; CNRS; INRA; Université de Lyon; Université Lyon 1, 69622 Villeurbanne, France, 5European Molecular Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany, 6Swiss Institute of Bioinformatics (SIB), CMU - Rue Michel-Servet 11211, Geneva 4, Switzerland, 7Department of Computer Science, University of Bristol, Woodland Road, Bristol, BS8 1UB, UK, 8J. Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, MD 20850, USA, 9Computational Biology Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Campus, Anzio Road, Observatory 7925, South Africa, 10University of Southern California, Los Angeles, CA 90089, USA, 11Protein Information Resource (PIR), Georgetown University Medical Center, 3300 Whitehaven Street, NW, Suite 1200 Washington, D.C. 20007, USA and 12Structural and Molecular Biology Department, University College London, University of London, WC1E 6BT UK
                Author notes
                *To whom correspondence should be addressed. Tel: +44 (0) 1223 494 481; Fax: +44 (0) 1223 494 468; Email: hunter@ 123456ebi.ac.uk
                Correspondence may also be addressed to Alex Mitchell. Email: mitchell@ 123456ebi.ac.uk
                Correspondence may also be addressed to Philip Jones. Tel: +44 (0) 1223 492610; Fax: +44 (0) 1223 494484; Email: pjones@ 123456ebi.ac.uk

                The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.

                Article
                Publisher ID: gkr948
                DOI: 10.1093/nar/gkr948
                PMC ID: 3245097
                PubMed ID: 22096229
                SO-VID: 82db4be3-d6e5-4ccd-b2b6-24d54f3e2c80
                Copyright © © The Author(s) 2011. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 4 October 2011
                Date revision received : 10 October 2011
                Date accepted : 12 October 2011
                Page count
                Pages: 7
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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