NDLI: Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study

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Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study

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Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study

Content Provider	ACM Digital Library
Author	El-Manzalawy, Yasser Honavar, Vasant Jordan, Rafael A. Xue, Li C. Dobbs, Drena
Abstract	Computational protein-protein docking is a valuable tool for determining the conformation of complexes formed by interacting proteins. Selecting near-native conformations from the large number of possible models generated by docking software presents a significant challenge in practice. We introduce a novel method for ranking docked conformations based on the degree of overlap between the interface residues of a docked conformation formed by a pair of proteins with the set of predicted interface residues between them. Our approach relies on a method, called PS-HomPPI, for reliably predicting proteinprotein interface residues by taking into account information derived from both interacting proteins. PS-HomPPI infers the residues of a query protein that are likely to interact with a partner protein based on known interface residues of the homo-interologs of the query-partner protein pair, i.e., pairs of interacting proteins that are homologous to the query protein and partner protein. Our results on Docking Benchmark 3.0 show that the quality of the ranking of docked conformations using our method is consistently superior to that produced using ClusPro cluster-size-based and energy-based criteria for 61 out of the 64 docking complexes for which PS-HomPPI produces interface predictions. An implementation of our method for ranking docked models is freely available at: http://einstein.cs.iastate.edu/DockRank/.
Starting Page	441
Ending Page	445
Page Count	5
File Format	PDF
ISBN	9781450307963
DOI	10.1145/2147805.2147866
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2011-08-01
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Protein-protein docking Docking scoring function
Content Type	Text
Resource Type	Article

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