Analysis of protein binding sites by computational solvent mapping.

ABSTRACT: Computational solvent mapping globally samples the surface of target proteins using molecular probes-small molecules or functional groups-to identify potentially favorable binding positions. The method is based on X-ray and NMR screening studies showing that the binding sites of proteins also bind a large variety of fragment-sized molecules. We have developed the multistage mapping algorithm FTMap (available as a server at http://ftmap.bu.edu/ ) based on the fast Fourier transform (FFT) correlation approach. Identifying regions of low free energy rather than individual low energy conformations, FTMap reproduces the available experimental mapping results. Applications to a variety of proteins show that the probes always cluster in import

SUBMITTER: Hall DR 

PROVIDER: S-EPMC3526383 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature