Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions.

ABSTRACT: The effects of solvation and entropy play a critical role in determining the binding free energy in protein-ligand interactions. Despite the good balance between speed and accuracy, no current knowledge-based scoring functions account for the effects of solvation and configurational entropy explicitly due to the difficulty in deriving the corresponding pair potentials and the resulting double counting problem. In the present work, we have included the solvation effect and configurational entropy in the knowledge-based scoring function by an iterative method. The newly developed scoring function has yielded a success rate of 91% in identifying near-native binding modes with Wang et al.'s benchmark of 100 diverse protein-ligand complexes. The results have been compared with the results of 15

SUBMITTER: Huang SY 

PROVIDER: S-EPMC3199178 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature