Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.

ABSTRACT: Characterizing large-scale structural transitions in biomolecular systems poses major technical challenges to both experimental and computational approaches. On the computational side, efficient sampling of the configuration space along the transition pathway remains the most daunting challenge. Recognizing this issue, we introduce a knowledge-based computational approach toward describing large-scale conformational transitions using (i) nonequilibrium, driven simulations combined with work measurements and (ii) free energy calculations using empirically optimized biasing protocols. The first part is based on designing mechanistically relevant, system-specific reaction coordinates whose usefulness and applicability in inducing the transition of interest are examined using knowledge-based,

SUBMITTER: Moradi M 

PROVIDER: S-EPMC4089915 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature