title: Performance Comparison of Systematic Methods for Rigorous Definition of Coarse-Grained Sites of Large Biomolecules.
abstract: Construction of coarse-grained (CG) models for large biomolecules used for multiscale simulations demands a rigorous definition of CG sites for them. Several coarse-graining methods such as the simulated annealing and steepest descent (SASD) based on the essential dynamics coarse-graining (ED-CG) or the stepwise local iterative optimization (SLIO) based on the fluctuation maximization coarse-graining (FM-CG), were developed to do it. However, the practical applications of these methods such as SASD based on ED-CG are subject to limitations because they are too expensive. In this work, we extend the applicability of ED-CG by combining it with the SLIO algorithm. A comprehensive comparison of optimized results and accuracy of various algorithms based on ED-CG show that SLIO is the fastest as well as the most accurate algorithm among them. ED-CG combined with SLIO could give converged results as the number of CG sites increases, which demonstrates that it is another efficient method for coarse-graining large biomolecules. The construction of CG sites for Ras protein by using MD fluctuations demonstrates that the CG sites derived from FM-CG can reflect the fluctuation properties of secondary structures in Ras accurately.
authors.affiliation: State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemistry Engineering, Xiamen University , Xiamen 361005, China.|School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.
authors.forename: Yuwei
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemistry Engineering, Xiamen University , Xiamen 361005, China.
authors.forename: Zexing
authors.initials: Z
authors.lastname: Cao
authors.affiliation: School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry, NYU Shanghai , Shanghai 200062, China.
authors.forename: John Zenghui
authors.initials: JZ
authors.lastname: Zhang
authors.affiliation: School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry, NYU Shanghai , Shanghai 200062, China.
authors.forename: Fei
authors.identifier: 0000-0001-9458-9175
authors.initials: F
authors.lastname: Xia
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D013997:Time Factors; D018631:ras Proteins / Q000737:chemistry*
chemical_list: D018631:ras Proteins