Ontology highlight
ABSTRACT:
SUBMITTER: Maurer M
PROVIDER: S-EPMC6220940 | biostudies-literature | 2018 Oct
REPOSITORIES: biostudies-literature
Journal of computational chemistry 20181002 26
We investigate the ability of several free-energy calculation methods to combine two alchemical changes. We use Bennett acceptance ratio (BAR), thermodynamic integration (TI), extended TI (X-TI), and enveloping distribution sampling (EDS) to perturb a water molecule, which is restrained to an amino acid that is also being perturbed. In addition to these pairwise methods, we present two two-dimensional approaches, EDS-TI and two-dimensional TI (2D-TI). We compare feasibility, efficiency and usabi ...[more]