Predicting Protein Interactions by Brownian Dynamics Simulations
Joint Authors
Zhang, Hong-Xing
Meng, Xuan-Yu
Cui, Meng
Mezei, Mihaly
Xu, Yu
Source
Journal of Biomedicine and Biotechnology
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-02-15
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Meng, Xuan-Yu& Xu, Yu& Zhang, Hong-Xing& Mezei, Mihaly& Cui, Meng. 2012. Predicting Protein Interactions by Brownian Dynamics Simulations. Journal of Biomedicine and Biotechnology،Vol. 2012, no. 2012, pp.1-11.
https://search.emarefa.net/detail/BIM-447294
Modern Language Association (MLA)
Meng, Xuan-Yu…[et al.]. Predicting Protein Interactions by Brownian Dynamics Simulations. Journal of Biomedicine and Biotechnology No. 2012 (2012), pp.1-11.
https://search.emarefa.net/detail/BIM-447294
American Medical Association (AMA)
Meng, Xuan-Yu& Xu, Yu& Zhang, Hong-Xing& Mezei, Mihaly& Cui, Meng. Predicting Protein Interactions by Brownian Dynamics Simulations. Journal of Biomedicine and Biotechnology. 2012. Vol. 2012, no. 2012, pp.1-11.
https://search.emarefa.net/detail/BIM-447294
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-447294