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

被引：810

作者：

Hunter, Sarah ^{[1
]}

Jones, Philip ^{[1
]}

Mitchell, Alex ^{[1
]}

Apweiler, Rolf ^{[1
]}

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

Bateman, Alex ^{[4
]}

Bernard, Thomas ^{[5
,6
]}

Binns, David ^{[1
]}

Bork, Peer ^{[7
]}

Burge, Sarah ^{[1
]}

de Castro, Edouard ^{[8
]}

Coggill, Penny ^{[4
]}

Corbett, Matthew ^{[1
]}

Das, Ujjwal ^{[1
]}

Daugherty, Louise ^{[1
]}

Duquenne, Lauranne ^{[5
,6
]}

Finn, Robert D. ^{[4
]}

Fraser, Matthew ^{[1
]}

Gough, Julian ^{[9
]}

Haft, Daniel ^{[10
]}

Hulo, Nicolas ^{[8
]}

Kahn, Daniel ^{[5
,6
]}

Kelly, Elizabeth ^{[11
]}

Letunic, Ivica ^{[7
]}

Lonsdale, David ^{[1
]}

Lopez, Rodrigo ^{[1
]}

Madera, Martin ^{[9
]}

Maslen, John ^{[1
]}

McAnulla, Craig ^{[1
]}

McDowall, Jennifer ^{[1
]}

McMenamin, Conor ^{[1
]}

Mi, Huaiyu ^{[12
]}

Mutowo-Muellenet, Prudence ^{[1
]}

Mulder, Nicola ^{[11
]}

Natale, Darren ^{[13
]}

Orengo, Christine ^{[14
]}

Pesseat, Sebastien ^{[1
]}

Punta, Marco ^{[4
]}

Quinn, Antony F. ^{[1
]}

Rivoire, Catherine ^{[8
]}

Sangrador-Vegas, Amaia ^{[1
]}

Selengut, Jeremy D. ^{[10
]}

Sigrist, Christian J. A. ^{[8
]}

Scheremetjew, Maxim ^{[1
]}

Tate, John ^{[4
]}

Thimmajanarthanan, Manjulapramila ^{[1
]}

Thomas, Paul D. ^{[12
]}

Wu, Cathy H. ^{[14
]}

Yeats, Corin ^{[14
]}

Yong, Siew-Yit ^{[1
]}

机构：

[1] EMBL, Outstat European Bioinformat Inst EBI, Cambridge CB10 1SD, England

[2] Univ Manchester, Fac Life Sci, Manchester M13 9PL, Lancs, England

[3] Univ Manchester, Sch Comp Sci, Manchester M13 9PL, Lancs, England

[4] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[5] Univ Lyon 1, CNRS, INRA, PRABI, F-69622 Villeurbanne, France

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

[7] European Mol Lab EMBL, D-69117 Heidelberg, Germany

[8] CMU, SIB, Geneva 4, Switzerland

[9] Univ Bristol, Dept Comp Sci, Bristol BS8 1UB, Avon, England

[10] JCVI, Rockville, MD 20850 USA

[11] Univ Cape Town, Inst Infect Dis & Mol Med, Computat Biol Unit, ZA-7925 Observatory, South Africa

[12] Univ So Calif, Los Angeles, CA 90089 USA

[13] Georgetown Univ, Med Ctr, PIR, Washington, DC 20007 USA

[14] Univ London, Univ Coll London, Struct & Mol Biol Dept, London WC1E 6BT, England

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / D1期

基金：

英国生物技术与生命科学研究理事会; 美国国家卫生研究院;

关键词：

GENE ONTOLOGY; PROTEIN FAMILIES; ANNOTATION; FRAMEWORK; PATHWAYS;

D O I：

10.1093/nar/gkr948

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：

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.

引用

页码：D306 / D312

页数：7

共 28 条

[1] Ongoing and future developments at the Universal Protein Resource [J].

Apweiler, Rolf ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Antunes, Ricardo ;

Barrell, Daniel ;

Bely, Benoit ;

Bingley, Mark ;

Binns, David ;

Bower, Lawrence ;

Browne, Paul ;

Chan, Wei Mun ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Fazzini, Francesco ;

Fedotov, Alexander ;

Foulger, Rebecca ;

Garavelli, John ;

Castro, Leyla Garcia ;

Huntley, Rachael ;

Jacobsen, Julius ;

Kleen, Michael ;

Laiho, Kati ;

Legge, Duncan ;

Lin, Quan ;

Liu, Wudong ;

Luo, Jie ;

Orchard, Sandra ;

Patient, Samuel ;

Pichler, Klemens ;

Poggioli, Diego ;

Pontikos, Nikolas ;

Pruess, Manuela ;

Rosanoff, Steven ;

Sawford, Tony ;

Sehra, Harminder ;

Turner, Edward ;

Corbett, Matt ;

Donnelly, Mike ;

van Rensburg, Pieter ;

Xenarios, Ioannis ;

Bougueleret, Lydie ;

Auchincloss, Andrea ;

Argoud-Puy, Ghislaine ;

Axelsen, Kristian ;

Bairoch, Amos ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D214-D219

[2] The IntAct molecular interaction database in 2010 [J].

Aranda, B. ;

Achuthan, P. ;

Alam-Faruque, Y. ;

Armean, I. ;

Bridge, A. ;

Derow, C. ;

Feuermann, M. ;

Ghanbarian, A. T. ;

Kerrien, S. ;

Khadake, J. ;

Kerssemakers, J. ;

Leroy, C. ;

Menden, M. ;

Michaut, M. ;

Montecchi-Palazzi, L. ;

Neuhauser, S. N. ;

Orchard, S. ;

Perreau, V. ;

Roechert, B. ;

van Eijk, K. ;

Hermjakob, H. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D525-D531

[3] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[4] 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

[5] The ENZYME database in 2000 [J].

Bairoch, A .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :304-305

[6]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]

[7] 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

[8] 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

[9] The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases [J].

Caspi, Ron ;

Altman, Tomer ;

Dale, Joseph M. ;

Dreher, Kate ;

Fulcher, Carol A. ;

Gilham, Fred ;

Kaipa, Pallavi ;

Karthikeyan, Athikkattuvalasu S. ;

Kothari, Anamika ;

Krummenacker, Markus ;

Latendresse, Mario ;

Mueller, Lukas A. ;

Paley, Suzanne ;

Popescu, Liviu ;

Pujar, Anuradha ;

Shearer, Alexander G. ;

Zhang, Peifen ;

Karp, Peter D. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D473-D479

[10] Enzyme-specific profiles for genome annotation: PRIAM [J].

Claudel-Renard, C ;

Chevalet, C ;

Faraut, T ;

Kahn, D .

NUCLEIC ACIDS RESEARCH, 2003, 31 (22) :6633-6639

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