Force field influences in beta-hairpin folding simulations.

ABSTRACT: All-atom force fields are now routinely used for more detailed understanding of protein folding mechanisms. However, it has been pointed out that use of all-atom force fields does not guarantee more accurate representations of proteins; in fact, sometimes it even leads to biased structural distributions. Indeed, several issues remain to be solved in force field developments, such as accurate treatment of implicit solvation for efficient conformational sampling and proper treatment of backbone interactions for secondary structure propensities. In this study, we first investigate the quality of several recently improved backbone interaction schemes in AMBER for folding simulations of a beta-hairpin peptide, and further study their influences on the peptide's folding mechanism. Due to the sig

SUBMITTER: Lwin TZ 

PROVIDER: S-EPMC2242415 | biostudies-literature | 2006 Nov

REPOSITORIES: biostudies-literature