Prediction of enzyme function by combining sequence similarity and protein interactions

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• dc.contributor.author Espadaler, Jordica
• dc.contributor.author Eswar, Narayananca
• dc.contributor.author Querol, Enriqueca
• dc.contributor.author Avilés, Francesc Xavierca
• dc.contributor.author Sali, Andrejca
• dc.contributor.author Martí Renom, Marc A.ca
• dc.contributor.author Oliva Miguel, Baldomeroca
• dc.date.accessioned 2012-05-09T08:42:56Z
• dc.date.available 2012-05-09T08:42:56Z
• dc.date.issued 2008ca
• dc.description.abstract Background: A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners. Results: The method has been tested against the PSI-BLAST program using a set of 3,890 protein sequences from which interaction data was available. For protein sequences that align with at least 40% sequence identity to a known enzyme, the specificity of our method in predicting the first three EC digits increased from 80% to 90% at 80% coverage when compared to PSI-BLAST. Conclusion: Our method can also be used in proteins for which homologous sequences with known interacting partners can be detected. Thus, our method could increase 10% the specificity of genome-wide enzyme predictions based on sequence matching by PSI-BLAST alone.
• dc.description.sponsorship JE was supported by predoctoral fellowship from the Generalitat de Catalunya and CERBA (Spain). EQ acknowledges grants from the Spanish Ministerio de Educación y Ciencia (BIO2007-67904-C02-01). FXA acknowledges grants from the Spanish Ministerio de Educación y Ciencia (BIO2007-68046). AS acknowledges the financial support by the Sandler Family Supporting Foundation, IBM, HP, Netapps, and Intel for hardware gifts, and NIH grants GM74945, GM74929, GM71790, and GM54762. MAM-R acknowledges support from the Spanish Ministerio de Educación y Ciencia (BIO2007-66670). BO acknowledges grants from Generalitat de Catalunya (CIDEM), Spanish Ministerio de Educación y Ciencia (MEC BIO2005-00533 and PROFIT PSE-010000-2007-1) and by European Union INFOBIOMED-NoE (IST-507585) and @NEURIST (IST-2004-027703)
• dc.format.mimetype application/pdfca
• dc.identifier.citation Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B. Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics. 2008;9:249. DOI: 10.1186/1471-2105-9-249ca
• dc.identifier.doi http://dx.doi.org/10.1186/1471-2105-9-249
• dc.identifier.issn 1471-2105ca
• dc.identifier.uri http://hdl.handle.net/10230/16432
• dc.language.iso engca
• dc.publisher BioMed Centralca
• dc.relation.ispartof BMC Bioinformatics. 2008;9:249
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2007-67904-C02-01
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2007-68046
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2007-66670
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP6/507585
• dc.rights © 2008 Espadaler et al. Creative Commons Attribution Licenseca
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/2.0/
• dc.subject.other Interaccions proteïna-proteïna
• dc.subject.other Proteïnes -- Anàlisi
• dc.title Prediction of enzyme function by combining sequence similarity and protein interactionsca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersion