Protein-Ligand CH-π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation.

ABSTRACT: Here, we develop an empirical energy function based on quantum mechanical data for the interaction between methane and benzene that captures the contribution from CH-π interactions. Such interactions are frequently observed in protein-ligand crystal structures, particularly for carbohydrate ligands, but have been hard to quantify due to the absence of a model for CH-π interactions in typical molecular mechanical force fields or docking scoring functions. The CH-π term was added to the AutoDock Vina (AD VINA) scoring function enabling its performance to be evaluated against a cohort of more than 1600 occurrences in 496 experimental structures of protein-ligand complexes. By employing a conformational grid search algorithm, inclusion of the CH-π term was shown to improve the prediction of th

SUBMITTER: Xiao Y 

PROVIDER: S-EPMC10448718 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature