Ontology highlight
ABSTRACT:
SUBMITTER: Mamonov AB
PROVIDER: S-EPMC3496292 | biostudies-literature | 2012 Aug
REPOSITORIES: biostudies-literature
Mamonov Artem B AB Lettieri Steven S Ding Ying Y Sarver Jessica L JL Palli Rohith R Cunningham Timothy F TF Saxena Sunil S Zuckerman Daniel M DM
Journal of chemical theory and computation 20120615 8
Building on our recently introduced library-based Monte Carlo (LBMC) approach, we describe a flexible protocol for mixed coarse-grained (CG)/all-atom (AA) simulation of proteins and ligands. In the present implementation of LBMC, protein side chain configurations are pre-calculated and stored in libraries, while bonded interactions along the backbone are treated explicitly. Because the AA side chain coordinates are maintained at minimal run-time cost, arbitrary sites and interaction terms can be ...[more]