RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology.

ABSTRACT: The calculation of relative binding free energies (RBFE) involves the choice of the end-state/system representation, of a sampling approach, and of a free-energy estimator. System representations are usually termed "single topology" or "dual topology". As the terminology is often used ambiguously in the literature, a systematic categorization of the system representations is proposed here. In the dual-topology approach, the molecules are simulated as separate molecules. Such an approach is relatively easy to automate for high-throughput RBFE calculations compared to the single-topology approach. Distance restraints are commonly applied to prevent the molecules from drifting apart, thereby improving the sampling efficiency. In this study, we introduce the program RestraintMaker, which relie

SUBMITTER: Ries B 

PROVIDER: S-EPMC8994745 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature