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Open Access Highly Accessed Research article

ASPDock: protein-protein docking algorithm using atomic solvation parameters model

Lin Li, Dachuan Guo, Yangyu Huang, Shiyong Liu* and Yi Xiao*

Author Affiliations

Biomolecular Physics and Modelling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, PR China

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BMC Bioinformatics 2011, 12:36  doi:10.1186/1471-2105-12-36

Published: 27 January 2011

Abstract

Background

Atomic Solvation Parameters (ASP) model has been proven to be a very successful method of calculating the binding free energy of protein complexes. This suggests that incorporating it into docking algorithms should improve the accuracy of prediction. In this paper we propose an FFT-based algorithm to calculate ASP scores of protein complexes and develop an ASP-based protein-protein docking method (ASPDock).

Results

The ASPDock is first tested on the 21 complexes whose binding free energies have been determined experimentally. The results show that the calculated ASP scores have stronger correlation (r ≈ 0.69) with the binding free energies than the pure shape complementarity scores (r ≈ 0.48). The ASPDock is further tested on a large dataset, the benchmark 3.0, which contain 124 complexes and also shows better performance than pure shape complementarity method in docking prediction. Comparisons with other state-of-the-art docking algorithms showed that ASP score indeed gives higher success rate than the pure shape complementarity score of FTDock but lower success rate than Zdock3.0. We also developed a softly restricting method to add the information of predicted binding sites into our docking algorithm. The ASP-based docking method performed well in CAPRI rounds 18 and 19.

Conclusions

ASP may be more accurate and physical than the pure shape complementarity in describing the feature of protein docking.