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Protein-peptide complex prediction through fragment interaction patterns

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dc.contributor.author Verschueren, Erik
dc.contributor.author Vanhee, Peter
dc.contributor.author Rousseau, Frédéric
dc.contributor.author Schymkowitz, Joost
dc.contributor.author Serrano Pubull, Luis, 1982-
dc.date.accessioned 2015-02-11T09:31:39Z
dc.date.available 2015-02-11T09:31:39Z
dc.date.issued 2013
dc.identifier.citation Verschueren E, Vanhee P, Rousseau F, Schymkowitz J, Serrano L. Protein-peptide complex prediction through fragment interaction patterns. Structure. 2013; 21(5): 789-97. DOI: 10.1016/j.str.2013.02.023
dc.identifier.issn 0969-2126
dc.identifier.uri http://hdl.handle.net/10230/23122
dc.description.abstract The number of protein-peptide interactions in a cell is so large that experimental determination of all these complex structures would be a daunting task. Although homology modeling and refinement protocols have vastly improved the number and quality of predicted structural models, ab initio methods are still challenged by both the large number of possible docking sites and the conformational space accessible to flexible peptides. We present a method that addresses these challenges by sampling the entire accessible surface of a protein with a reduced conformational space of interacting backbone fragment pairs from unrelated structures. We demonstrate its potential by predicting ab initio the bound structure for a variety of protein-peptide complexes. In addition, we show the potential of our method for the discovery of domain interaction sites and domain-domain docking.
dc.description.sponsorship Research for this article was funded by a PhD scholarship from the EU grant Penelope FW6, funding from the EU grants 3D repertoire and PROSPECTS (grant agreement number HEALTHF4- 2008-201648) and the Spanish grant Centrosome3D (to E.V.)
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Elsevier
dc.rights © Elsevier http://dx.doi.org/10.1016/j.str.2013.02.023 Article published under an Elsevier user license, protected by copyright and may be used for non-commercial purposes. Users may access, download, copy, translate, text mine and data mine the article.
dc.rights.uri http://www.elsevier.com/open-access/userlicense/1.0/
dc.subject.other Pèptids
dc.subject.other Proteïnes
dc.subject.other Química
dc.title Protein-peptide complex prediction through fragment interaction patterns
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1016/j.str.2013.02.023
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/201648
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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