The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

ABSTRACT: Approaches for computing small molecule binding free energies based on molecular simulations are now regularly being employed by academic and industry practitioners to study receptor-ligand systems and prioritize the synthesis of small molecules for ligand design. Given the variety of methods and implementations available, it is natural to ask how the convergence rates and final predictions of these methods compare. In this study, we describe the concept and results for the SAMPL6 SAMPLing challenge, the first challenge from the SAMPL series focusing on the assessment of convergence properties and reproducibility of binding free energy methodologies. We provided parameter files, partial charges, and multiple initial geometries for two octa-acid (OA) and one cucurbit[8]uril (CB8) host-guest

SUBMITTER: Rizzi A 

PROVIDER: S-EPMC7282318 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature