Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis.

ABSTRACT: The goal of this work is to learn from nature about the magnitudes of side-chain motions that occur when proteins bind small organic molecules, and model these motions to improve the prediction of protein-ligand complexes. Following analysis of protein side-chain motions upon ligand binding in 63 complexes, we tested the ability of the docking tool SLIDE to model these motions without being restricted to rotameric transitions or deciding which side chains should be considered as flexible. The model tested is that side-chain conformational changes involving more atoms or larger rotations are likely to be more costly and less prevalent than small motions due to energy barriers between rotamers and the potential of large motions to cause new steric clashes. Accordingly, SLIDE adjusts the prot

SUBMITTER: Zavodszky MI 

PROVIDER: S-EPMC2253453 | biostudies-literature | 2005 Apr

REPOSITORIES: biostudies-literature