dc.contributor.author |
Espadaler, Jordi |
dc.contributor.author |
Eswar, Narayanan |
dc.contributor.author |
Querol, Enrique |
dc.contributor.author |
Avilés, Francesc Xavier |
dc.contributor.author |
Sali, Andrej |
dc.contributor.author |
Martí Renom, Marc A. |
dc.contributor.author |
Oliva Miguel, Baldomero |
dc.date.accessioned |
2012-05-09T08:42:56Z |
dc.date.available |
2012-05-09T08:42:56Z |
dc.date.issued |
2008 |
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: 10.1186/1471-2105-9-249 |
dc.identifier.issn |
1471-2105 |
dc.identifier.uri |
http://hdl.handle.net/10230/16432 |
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/pdf |
dc.language.iso |
eng |
dc.publisher |
BioMed Central |
dc.relation.ispartof |
BMC Bioinformatics. 2008;9:249 |
dc.rights |
© 2008 Espadaler et al. Creative Commons Attribution License |
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 interactions |
dc.type |
info:eu-repo/semantics/article |
dc.identifier.doi |
http://dx.doi.org/10.1186/1471-2105-9-249 |
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.accessRights |
info:eu-repo/semantics/openAccess |
dc.type.version |
info:eu-repo/semantics/publishedVersion |