FTMAP: extended protein mapping with user-selected probe molecules.

ABSTRACT: Binding hot spots, protein sites with high-binding affinity, can be identified using X-ray crystallography or NMR by screening libraries of small organic molecules that tend to cluster at such regions. FTMAP, a direct computational analog of the experimental screening approaches, globally samples the surface of a target protein using small organic molecules as probes, finds favorable positions, clusters the conformations and ranks the clusters on the basis of the average energy. The regions that bind several probe clusters predict the binding hot spots, in good agreement with experimental results. Small molecules discovered by fragment-based approaches to drug design also bind at the hot spot regions. To identify such molecules and their most likely bound positions, we extend the functiona

SUBMITTER: Ngan CH 

PROVIDER: S-EPMC3394268 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature