SDOCK: A Global Protein-Protein Docking Program Using Stepwise   Force-Field Potentials

doi:10.1002/jcc.21839

CORC > 北京大学 > 化学与分子工程学院

	SDOCK: A Global Protein-Protein Docking Program Using Stepwise Force-Field Potentials
	Zhang, Changsheng ; Lai, Luhua
刊名	journal of computational chemistry
	2011
关键词	protein-protein docking stepwise potentials force-field potentials protein interaction Lazaridis-Karplus desolvation SHAPE-COMPLEMENTARITY CRYSTAL-STRUCTURE GEOMETRIC FIT DATA-BANK COMPLEXES ELECTROSTATICS DESIGN PREDICTIONS ALGORITHM LIGANDS
DOI	10.1002/jcc.21839
英文摘要	Fast 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; http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000293110700009&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701 ; Chemistry, Multidisciplinary; SCI(E); EI; PubMed; 10; ARTICLE; 12; 2598-2612; 32
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/149965]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Zhang, Changsheng,Lai, Luhua. SDOCK: A Global Protein-Protein Docking Program Using Stepwise Force-Field Potentials[J]. journal of computational chemistry,2011.
APA	Zhang, Changsheng,&Lai, Luhua.(2011).SDOCK: A Global Protein-Protein Docking Program Using Stepwise Force-Field Potentials.journal of computational chemistry.
MLA	Zhang, Changsheng,et al."SDOCK: A Global Protein-Protein Docking Program Using Stepwise Force-Field Potentials".journal of computational chemistry (2011).