Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations.

ABSTRACT: The Drug Design Data Resource (D3R) consortium organises blinded challenges to address the latest advances in computational methods for ligand pose prediction, affinity ranking, and free energy calculations. Within the context of the second D3R Grand Challenge several blinded binding free energies predictions were made for two congeneric series of Farsenoid X Receptor (FXR) inhibitors with a semi-automated alchemical free energy calculation workflow featuring FESetup and SOMD software tools. Reasonable performance was observed in retrospective analyses of literature datasets. Nevertheless, blinded predictions on the full D3R datasets were poor due to difficulties encountered with the ranking of compounds that vary in their net-charge. Performance increased for predictions that were restric

SUBMITTER: Mey ASJS 

PROVIDER: S-EPMC5767197 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature