InterPro: the integrative protein signature database

被引：1541

作者：

Hunter, Sarah ^{[1
]}

Apweiler, Rolf ^{[1
]}

Attwood, Teresa K. ^{[2
,3
]}

Bairoch, Amos ^{[4
]}

Bateman, Alex ^{[5
]}

Binns, David ^{[1
]}

Bork, Peer ^{[6
]}

Das, Ujjwal ^{[1
]}

Daugherty, Louise ^{[1
]}

Duquenne, Lauranne ^{[7
,8
]}

Finn, Robert D. ^{[5
]}

Gough, Julian ^{[9
]}

Haft, Daniel ^{[10
]}

Hulo, Nicolas ^{[4
]}

Kahn, Daniel

Kelly, Elizabeth ^{[11
]}

Laugraud, Aurelie ^{[7
,8
]}

Letunic, Ivica ^{[6
]}

Lonsdale, David ^{[1
]}

Lopez, Rodrigo ^{[1
]}

Madera, Martin ^{[9
]}

Maslen, John ^{[1
]}

McAnulla, Craig ^{[1
]}

McDowall, Jennifer ^{[1
]}

Mistry, Jaina ^{[5
]}

Mitchell, Alex ^{[1
,2
,3
]}

Mulder, Nicola ^{[11
]}

Natale, Darren ^{[12
]}

Orengo, Christine ^{[13
]}

Quinn, Antony F. ^{[1
]}

Selengut, Jeremy D. ^{[10
]}

Sigrist, Christian J. A. ^{[4
]}

Thimma, Manjula ^{[1
]}

Thomas, Paul D. ^{[14
]}

Valentin, Franck ^{[1
]}

Wilson, Derek ^{[15
]}

Wu, Cathy H. ^{[12
]}

Yeats, Corin

机构：

[1] EBI, EMBL Outstn, Hinxton, Cambs, England

[2] Univ Manchester, Fac Life Sci, Manchester, Lancs, England

[3] Univ Manchester, Sch Comp Sci, Manchester, Lancs, England

[4] SIB, Geneva, Switzerland

[5] Wellcome Trust Sanger Inst, Cambridge, England

[6] European Mol Lab EMBL, Heidelberg, Germany

[7] Univ Lyon 1, CNRS, INRIA, Pole Rhone Alpins Bioinformat PRABI, F-69622 Villeurbanne, France

[8] Univ Lyon 1, CNRS, INRIA, Lab Biometrie & Biol Evolut, F-69622 Villeurbanne, France

[9] Univ Bristol, Dept Comp Sci, Bristol, Avon, England

[10] JCVI, Rockville, MD 20850 USA

[11] Univ Cape Town, Computat Biol Unit, ZA-7700 Rondebosch, South Africa

[12] Georgetown Univ, Med Ctr, Washington, DC 20007 USA

[13] UCL, Dept Biol Mol & Struct, London, England

[14] SRI Int, Evolutionary Syst Biol, Menlo Pk, CA 94025 USA

[15] MRC, Mol Biol Lab, Cambridge, England

来源：

NUCLEIC ACIDS RESEARCH | 2009年 / 37卷

基金：

英国生物技术与生命科学研究理事会;

关键词：

FAMILIES; DOMAINS;

D O I：

10.1093/nar/gkn785

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total similar to 58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/).

引用

页码：D211 / D215

页数：5

共 26 条

[1] PRINTS and its automatic supplement, prePRINTS [J].

Attwood, TK ;

Bradley, P ;

Flower, DR ;

Gaulton, A ;

Maudling, N ;

Mitchell, AL ;

Moulton, G ;

Nordle, A ;

Paine, K ;

Taylor, P ;

Uddin, A ;

Zygouri, C .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :400-402

[2] The Universal Protein Resource (UniProt) [J].

Bairoch, Amos ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Puy, Ghislaine Argoud ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

Saux, Virginie Bulliard-Le ;

decastro, Edouard ;

Ciampina, Luciane ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

David, Fabrice ;

Delbard, Gwennaelle ;

Dornevil, Dolnide ;

Duek-Roggli, Paula ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Feuermann, Marc ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gehant, Sebastian ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

Innocenti, Alessandro ;

James, Janet ;

Jain, Eric ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D190-D195

[3] The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data [J].

Berman, Helen ;

Henrick, Kim ;

Nakamura, Haruki ;

Markley, John L. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D301-D303

[4] Genome sequence of babesia bovis and comparative analysis of apicomplexan hemoprotozoa [J].

Brayton, Kelly A. ;

Lau, Audrey O. T. ;

Herndon, David R. ;

Hannick, Linda ;

Kappmeyer, Lowell S. ;

Berens, Shawn J. ;

Bidwell, Shelby L. ;

Brown, Wendy C. ;

Crabtree, Jonathan ;

Fadrosh, Doug ;

Feldblum, Tamara ;

Forberger, Heather A. ;

Haas, Brian J. ;

Howell, Jeanne M. ;

Khouri, Hoda ;

Koo, Hean ;

Mann, David J. ;

Norimine, Junzo ;

Paulsen, Ian T. ;

Radune, Diana ;

Ren, Qinghu ;

Smith, Roger K., Jr. ;

Suarez, Carlos E. ;

White, Owen ;

Wortman, Jennifer R. ;

Knowles, Donald P., Jr. ;

McElwain, Terry F. ;

Nene, Vishvanath M. .

PLOS PATHOGENS, 2007, 3 (10) :1401-1413

[5] The ProDom database of protein domain families: more emphasis on 3D [J].

Bru, C ;

Courcelle, E ;

Carrre, S ;

Beausse, Y ;

Dalmar, S ;

Kahn, D .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D212-D215

[6] The Pfam protein families database [J].

Finn, Robert D. ;

Tate, John ;

Mistry, Jaina ;

Coggill, Penny C. ;

Sammut, Stephen John ;

Hotz, Hans-Rudolf ;

Ceric, Goran ;

Forslund, Kristoffer ;

Eddy, Sean R. ;

Sonnhammer, Erik L. L. ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D281-D288

[7] Curated genome annotation of Oryza sativa ssp japonica and comparative genome analysis with Arabidopsis thaliana -: The Rice Annotation Project [J].

Gojobori, Takashi .

GENOME RESEARCH, 2007, 17 (02) :175-183

[8] The TIGRFAMs database of protein families [J].

Haft, DH ;

Selengut, JD ;

White, O .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :371-373

[9] The Gene Ontology (GO) database and informatics resource [J].

Harris, MA ;

Clark, J ;

Ireland, A ;

Lomax, J ;

Ashburner, M ;

Foulger, R ;

Eilbeck, K ;

Lewis, S ;

Marshall, B ;

Mungall, C ;

Richter, J ;

Rubin, GM ;

Blake, JA ;

Bult, C ;

Dolan, M ;

Drabkin, H ;

Eppig, JT ;

Hill, DP ;

Ni, L ;

Ringwald, M ;

Balakrishnan, R ;

Cherry, JM ;

Christie, KR ;

Costanzo, MC ;

Dwight, SS ;

Engel, S ;

Fisk, DG ;

Hirschman, JE ;

Hong, EL ;

Nash, RS ;

Sethuraman, A ;

Theesfeld, CL ;

Botstein, D ;

Dolinski, K ;

Feierbach, B ;

Berardini, T ;

Mundodi, S ;

Rhee, SY ;

Apweiler, R ;

Barrell, D ;

Camon, E ;

Dimmer, E ;

Lee, V ;

Chisholm, R ;

Gaudet, P ;

Kibbe, W ;

Kishore, R ;

Schwarz, EM ;

Sternberg, P ;

Gwinn, M .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D258-D261

[10] The PROSITE database [J].

Hulo, Nicolas ;

Bairoch, Amos ;

Bulliard, Virginie ;

Cerutti, Lorenzo ;

De Castro, Edouard ;

Langendijk-Genevaux, Petra S. ;

Pagni, Marco ;

Sigrist, Christian J. A. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D227-D230

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