PACE Force Field for Protein Simulations. 1. Full Parameterization of   Version 1 and Verification

doi:10.1021/ct1003127

CORC > 北京大学 > 化学与分子工程学院

	PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification
	Han, Wei ; Wan, Cheuk-Kin ; Jiang, Fan ; Wu, Yun-Dong
刊名	journal of chemical theory and computation
	2010
关键词	MOLECULAR-DYNAMICS SIMULATIONS COARSE-GRAINED MODEL ACID SIDE-CHAINS MEAN FORCE ALL-ATOM BIOMOLECULAR SIMULATIONS STRUCTURE PREDICTION IMPLICIT SOLVENT PEPTIDE BACKBONE HYDROGEN-BONDS
DOI	10.1021/ct1003127
英文摘要	A further parametrization of a united-atom protein model coupled with coarse-grained water has been carried out to cover all amino acids (AAs). The local conformational features of each AA have been fitted on the basis of restricted coil-library statistics of high-resolution X-ray crystal structures of proteins. Potential functions were developed on the basis of combined backbone and side chain rotamer conformational preferences, or rotamer Ramachandran plots (phi, psi, chi 1). Side chain-side chain and side chain backbone interaction potentials were parametrized to fit the potential mean forces of corresponding all-atom simulations. The force field has been applied in molecular dynamics simulations of several proteins of 56-108 AA residues whose X-ray crystal and/or NMR structures are available. Starting from the crystal structures, each protein was simulated for about 100 ns. The C alpha RMSDs of the calculated structures are 2.4-4.2 angstrom with respect to the crystal and/or NMR structures, which are still larger than but close to those of all-atom simulations (1.1-3.6 angstrom). Starting from the PDB structure of malate synthase G of 723 AA residues, the wall-clock time of a 30 ns simulation is about three days on a 2.65 GHz dual-core CPU. The RMSD to the experimental structure is about 4.3 angstrom. These results implicate the applicability of the force field in the study of protein structures.; Chemistry, Physical; Physics, Atomic, Molecular & Chemical; SCI(E); 13; ARTICLE; 11,3285; 3373-3389; 6
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/242103]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Han, Wei,Wan, Cheuk-Kin,Jiang, Fan,et al. PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification[J]. journal of chemical theory and computation,2010.
APA	Han, Wei,Wan, Cheuk-Kin,Jiang, Fan,&Wu, Yun-Dong.(2010).PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification.journal of chemical theory and computation.
MLA	Han, Wei,et al."PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification".journal of chemical theory and computation (2010).