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Journal of Biomedicine and Biotechnology
Volume 2012 (2012), Article ID 121034, 11 pages
http://dx.doi.org/10.1155/2012/121034
Research Article

Predicting Protein Interactions by Brownian Dynamics Simulations

1Department of Physiology and Biophysics, Virginia Commonwealth University, 1220 East Broad Street, P.O. Box 980551, Richmond, VA 23298, USA
2State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
3Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA

Received 15 July 2011; Accepted 19 October 2011

Academic Editor: Sergio Pantano

Copyright © 2012 Xuan-Yu Meng et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation effects. The performance of this BD protein docking approach has been evaluated on a test set of 24 crystal protein complexes. Reproduction of experimental structures in the test set indicates the adequate conformational sampling and accurate scoring of this BD protein docking approach. Furthermore, we have developed an approach to account for the flexibility of proteins, which has been successfully applied to reproduce the experimental complex structure from the structure of two unbounded proteins. These results indicate that this adapted BD protein docking approach can be useful for the prediction of protein-protein interactions.