Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

ABSTRACT: Predicting protein-ligand binding affinities and the associated thermodynamics of biomolecular recognition is a primary objective of structure-based drug design. Alchemical free energy simulations offer a highly accurate and computationally efficient route to achieving this goal. While the AMBER molecular dynamics package has successfully been used for alchemical free energy simulations in academic research groups for decades, widespread impact in industrial drug discovery settings has been minimal because of the previous limitations within the AMBER alchemical code, coupled with challenges in system setup and postprocessing workflows. Through a close academia-industry collaboration we have addressed many of the previous limitations with an aim to improve accuracy, efficiency, and robustne

SUBMITTER: Lee TS 

PROVIDER: S-EPMC7686026 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature