Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy.

ABSTRACT: Protein-protein binding is fundamental to most biological processes. It is important to be able to use computation to accurately estimate the change in protein-protein binding free energy due to mutations in order to answer biological questions that would be experimentally challenging, laborious, or time-consuming. Although nonrigorous free-energy methods are faster, rigorous alchemical molecular dynamics-based methods are considerably more accurate and are becoming more feasible with the advancement of computer hardware and molecular simulation software. Even with sufficient computational resources, there are still major challenges to using alchemical free-energy methods for protein-protein complexes, such as generating hybrid structures and topologies, maintaining a neutral net charge of

SUBMITTER: Patel D 

PROVIDER: S-EPMC8044032 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature