Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions.

ABSTRACT: The reliability of molecular mechanics simulations to predict effects of ion binding to proteins depends on their ability to simultaneously describe ion-protein, ion-water, and protein-water interactions. Force fields (FFs) to describe protein-water and ion-water interactions have been constructed carefully and have also been refined routinely to improve accuracy. Descriptions for ion-protein interactions have also been refined, although in an a posteriori manner through the use of "nonbonded-fix (NB-fix)" approaches in which parameters from default Lennard-Jones mixing rules are replaced with those optimized against some reference data. However, even after NB-fix corrections, there remains a significant need for improvement. This is also true for polarizable FFs that include self-c

SUBMITTER: Delgado JA 

PROVIDER: S-EPMC9817009 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature