SDOCK: A Global Protein-Protein Docking Program Using Stepwise Force-Field Potentials
Zhang, Changsheng1; Lai, Luhua1,2
AbstractFast Fourier transform (FFT) method limits the forms of scoring functions in global protein-protein docking. On the other hand, force field potentials can effectively describe the energy hyper surface of biological macromolecules. In this study, we developed a new protein-protein docking program, SDOCK, that incorporates van der Waals attractive potential, geometric collision, screened electrostatic potential, and Lazaridis-Karplus desolvation energy into the scoring function in the global searching process. Stepwise potentials were generated from the corresponding continuous forms to treat the structure flexibility. After optimization of the atom solvation parameters and the weights of different potential terms based on a new docking test set that contains 142 cases with small or moderate conformational changes upon binding, SDOCK slightly outperformed the well-known FFT based global docking program ZDOCK3.0. Among the 142 cases tested, 52.8% gave at least one near-native solutions in the top 100 solutions. SDOCK was also tested on six blind testing cases in Critical Assessment of Predicted Interactions rounds 13 to 18. In all six cases, the near-native solutions could be found within the top 350 solutions. Because the SDOCK approach performs global docking based on force-field potentials, one of its advantages is that it provides global binding free energy surface profiles for further analysis. The efficiency of the program is also comparable with that of other FFT based protein-protein docking programs. SDOCK is available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi-bin/down.cgi. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2598-2612, 2011
KeywordProtein-protein Docking Stepwise Potentials Force-field Potentials Protein Interaction Lazaridis-karplus Desolvation
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WOS IDWOS:000293110700009
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Cited Times:23[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Corresponding AuthorLai, Luhua
Affiliation1.Peking Univ, Beijing Natl Lab Mol Sci, Coll Chem & Mol Engn, State Key Lab Struct Chem Unstable & Stable Speci, Beijing 100871, Peoples R China
2.Peking Univ, Ctr Theoret Biol, Beijing 100871, Peoples R China
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Zhang, Changsheng,Lai, Luhua. SDOCK: A Global Protein-Protein Docking Program Using Stepwise Force-Field Potentials[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY,2011,32(12):2598-2612.
APA Zhang, Changsheng,&Lai, Luhua.(2011).SDOCK: A Global Protein-Protein Docking Program Using Stepwise Force-Field Potentials.JOURNAL OF COMPUTATIONAL CHEMISTRY,32(12),2598-2612.
MLA Zhang, Changsheng,et al."SDOCK: A Global Protein-Protein Docking Program Using Stepwise Force-Field Potentials".JOURNAL OF COMPUTATIONAL CHEMISTRY 32.12(2011):2598-2612.
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