Xinqi Gong and Panwen Wang both are first authors.
Protein–protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring†
Article first published online: 23 JUL 2010
Copyright © 2010 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Special Issue: Fourth Meeting on the Critical Assessment of PRedicted Interactions
Volume 78, Issue 15, pages 3150–3155, 15 November 2010
How to Cite
Gong, X., Wang, P., Yang, F., Chang, S., Liu, B., He, H., Cao, L., Xu, X., Li, C., Chen, W. and Wang, C. (2010), Protein–protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring. Proteins, 78: 3150–3155. doi: 10.1002/prot.22831
The authors state no conflict of interest.
- Issue published online: 23 JUL 2010
- Article first published online: 23 JUL 2010
- Manuscript Accepted: 23 JUN 2010
- Manuscript Revised: 16 JUN 2010
- Manuscript Received: 31 MAR 2010
- Chinese Natural Science Foundation. Grant Numbers: 20773006, 10974008
- Research Fund for the Doctoral Program of Higher Education. Grant Number: 200800050003
- Beijing Natural Science Foundation. Grant Number: 4102006
- Fundamental Research Fund for the Beijing Municipal Education Commission Science and Technology Innovation Platform
- protein–protein docking;
- binding site prediction;
Protein–protein docking has made much progress in recent years, but challenges still exist. Here we present the application of our docking approach HoDock in CAPRI. In this approach, a binding site prediction is implemented to reduce docking sampling space and filter out unreasonable docked structures, and a network-based enhanced combinatorial scoring function HPNCscore is used to evaluate the decoys. The experimental information was combined with the predicted binding site to pick out the most likely key binding site residues. We applied the HoDock method in the recent rounds of the CAPRI experiments, and got good results as predictors on targets 39, 40, and 41. We also got good results as scorers on targets 35, 37, 40, and 41. This indicates that our docking approach can contribute to the progress of protein–protein docking methods and to the understanding of the mechanism of protein–protein interactions. Proteins 2010. © 2010 Wiley-Liss, Inc.