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A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys

By Shide Liang, Song Liu, Chi Zhang and Yaoqi Zhou

Abstract

Near-native selections from docking decoys have proved challenging especially when unbound proteins are used in the molecular docking. One reason is that significant atomic clashes in docking decoys lead to poor predictions of binding affinities of near native decoys. Atomic clashes can be removed by structural refinement through energy minimization. Such an energy minimization, however, will lead to an unrealistic bias toward docked structures with large interfaces. Here, we extend an empirical energy function developed for protein design to protein–protein docking selection by introducing a simple reference state that removes the unrealistic dependence of binding affinity of docking decoys on the buried solvent accessible surface area of interface. The energy function called EMPIRE (EMpirical Protein-InteRaction Energy), when coupled with a refinement strategy, is found to provide a significantly improved success rate in near native selections when applied to RosettaDock and refined ZDOCK docking decoys. Our work underlines the importance of removing nonspecific interactions from specific ones in near native selections from docking decoys

Topics: Research Article
Publisher: Wiley Subscription Services, Inc., A Wiley Company
OAI identifier: oai:pubmedcentral.nih.gov:2673351
Provided by: PubMed Central
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    Citations

    1. Modeling of protein interactions in genomes.
    2. Prediction of protein–protein interactions by docking methods.
    3. Principles of docking: an overview of search algorithms and a guide to scoring functions.
    4. Protein–protein association kinetics and protein docking.

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