Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility

摘要

Side chain sampling and optimization algorithms, mostly based on a rotamer approximation, have been used extensively in modeling proteins. One important application is homology modeling, where the backbone configuration is given from a related sequence, and the side chain configurations remain to be predicted. A second important application is modeling conformational changes due to ligand binding. In a recent article, Sherman et al. described a method for predicting “induced fit” effects by combining a docking program with protein side chain rotamer sampling, in an iterative fashion.