Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.

ABSTRACT: We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein-ligand complexes w

SUBMITTER: Deng N 

PROVIDER: S-EPMC5869689 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature