title: From laws of inference to protein folding dynamics.
abstract: Protein folding dynamics is one of major issues constantly investigated in the study of protein functions. The molecular dynamic (MD) simulation with the replica exchange method (REM) is a common theoretical approach considered. Yet a trade-off in applying the REM is that the dynamics toward the native configuration in the simulations seems lost. In this work, we show that given REM-MD simulation results, protein folding dynamics can be directly derived from laws of inference. The applicability of the resulting approach, the entropic folding dynamics, is illustrated by investigating a well-studied Trp-cage peptide. Our results are qualitatively comparable with those from other studies. The current studies suggest that the incorporation of laws of inference and physics brings in a comprehensive perspective on exploring the protein folding dynamics.
authors.affiliation: Graduate Institute of Systems Biology and Bioinformatics, National Central University, Chungli, Taiwan. chih-yuan.tseng@ualberta.ca
authors.forename: Chih-Yuan
authors.initials: CY
authors.lastname: Tseng
authors.forename: Chun-Ping
authors.initials: CP
authors.lastname: Yu
authors.forename: H C
authors.initials: HC
authors.lastname: Lee
mesh_terms: D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D011506:Proteins