Detecting mutually exclusive interactions in protein-protein interaction maps.

Handle URI:
http://hdl.handle.net/10754/596839
Title:
Detecting mutually exclusive interactions in protein-protein interaction maps.
Authors:
Sánchez Claros, Carmen; Tramontano, Anna
Abstract:
Comprehensive protein interaction maps can complement genetic and biochemical experiments and allow the formulation of new hypotheses to be tested in the system of interest. The computational analysis of the maps may help to focus on interesting cases and thereby to appropriately prioritize the validation experiments. We show here that, by automatically comparing and analyzing structurally similar regions of proteins of known structure interacting with a common partner, it is possible to identify mutually exclusive interactions present in the maps with a sensitivity of 70% and a specificity higher than 85% and that, in about three fourth of the correctly identified complexes, we also correctly recognize at least one residue (five on average) belonging to the interaction interface. Given the present and continuously increasing number of proteins of known structure, the requirement of the knowledge of the structure of the interacting proteins does not substantially impact on the coverage of our strategy that can be estimated to be around 25%. We also introduce here the Estrella server that embodies this strategy, is designed for users interested in validating specific hypotheses about the functional role of a protein-protein interaction and it also allows access to pre-computed data for seven organisms.
Citation:
Sánchez Claros C, Tramontano A (2012) Detecting Mutually Exclusive Interactions in Protein-Protein Interaction Maps. PLoS ONE 7: e38765. Available: http://dx.doi.org/10.1371/journal.pone.0038765.
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
KAUST Grant Number:
KUK-I1-012-43
Issue Date:
8-Jun-2012
DOI:
10.1371/journal.pone.0038765
PubMed ID:
22715412
PubMed Central ID:
PMC3370996
Type:
Article
ISSN:
1932-6203
Sponsors:
Award number KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorSánchez Claros, Carmenen
dc.contributor.authorTramontano, Annaen
dc.date.accessioned2016-02-21T09:35:08Zen
dc.date.available2016-02-21T09:35:08Zen
dc.date.issued2012-06-08en
dc.identifier.citationSánchez Claros C, Tramontano A (2012) Detecting Mutually Exclusive Interactions in Protein-Protein Interaction Maps. PLoS ONE 7: e38765. Available: http://dx.doi.org/10.1371/journal.pone.0038765.en
dc.identifier.issn1932-6203en
dc.identifier.pmid22715412en
dc.identifier.doi10.1371/journal.pone.0038765en
dc.identifier.urihttp://hdl.handle.net/10754/596839en
dc.description.abstractComprehensive protein interaction maps can complement genetic and biochemical experiments and allow the formulation of new hypotheses to be tested in the system of interest. The computational analysis of the maps may help to focus on interesting cases and thereby to appropriately prioritize the validation experiments. We show here that, by automatically comparing and analyzing structurally similar regions of proteins of known structure interacting with a common partner, it is possible to identify mutually exclusive interactions present in the maps with a sensitivity of 70% and a specificity higher than 85% and that, in about three fourth of the correctly identified complexes, we also correctly recognize at least one residue (five on average) belonging to the interaction interface. Given the present and continuously increasing number of proteins of known structure, the requirement of the knowledge of the structure of the interacting proteins does not substantially impact on the coverage of our strategy that can be estimated to be around 25%. We also introduce here the Estrella server that embodies this strategy, is designed for users interested in validating specific hypotheses about the functional role of a protein-protein interaction and it also allows access to pre-computed data for seven organisms.en
dc.description.sponsorshipAward number KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.publisherPublic Library of Science (PLoS)en
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.subject.meshModels, Geneticen
dc.subject.meshDatabases, Proteinen
dc.titleDetecting mutually exclusive interactions in protein-protein interaction maps.en
dc.typeArticleen
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC3370996en
dc.contributor.institutionDepartment of Physics, Sapienza University of Rome, Rome, Italy.en
kaust.grant.numberKUK-I1-012-43en

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