On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.
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ABSTRACT:
SUBMITTER: Menzer WM
PROVIDER: S-EPMC7311925 | biostudies-literature | 2020 Mar
REPOSITORIES: biostudies-literature
Publications
On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.
Menzer William M WM Xie Bing B Minh David D L DDL
Journal of computational chemistry 20191210 6
The impact of harmonic restraints on protein heavy atoms and ligand atoms on end-point free energy calculations is systematically characterized for 54 protein-ligand complexes. We observe that stronger restraints reduce the equilibration time and statistical inefficiency, suppress conformational sampling, influence correlation with experiment, and monotonically decrease the estimated loss of entropy upon binding, leading to stronger estimated binding free energies in most systems. A statistical ...[more]
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