Title:
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Protein-peptide complex prediction through fragment interaction patterns
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Author:
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Verschueren, Erik; Vanhee, Peter; Rousseau, Frédéric; Schymkowitz, Joost; Serrano Pubull, Luis, 1982-
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Abstract:
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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. |
Abstract:
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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.) |
Subject(s):
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-Pèptids -Proteïnes -Química |
Rights:
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© 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.
http://www.elsevier.com/open-access/userlicense/1.0/ |
Document type:
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Article Article - Published version |
Published by:
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Elsevier
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