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

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 indee...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Lin Li, Dachuan Guo, Yangyu Huang, Shiyong Liu, Yi Xiao
• Keywords: Artificial Intelligence, BMCBI 2011, Docking Algorithms, Protein Complexes, Pure Shape Complementarity