Document Type
Article
Original Publication Date
2012
Journal/Book/Conference Title
Journal of Biomedicine and Biotechnology
Volume
2012
DOI of Original Publication
10.1155/2012/121034
Date of Submission
August 2014
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.
Rights
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.
Is Part Of
VCU Physiology and Biophysics Publications
Comments
Originally published at http://dx.doi.org/10.1155/2012/121034