BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures.

ABSTRACT: Molecular docking serves as an important tool in modeling protein-ligand interactions. However, it is still challenging to incorporate overall receptor flexibility, especially backbone flexibility, in docking due to the large conformational space that needs to be sampled. To overcome this problem, we developed a novel flexible docking approach, BP-Dock (Backbone Perturbation-Dock) that can integrate both backbone and side chain conformational changes induced by ligand binding through a multi-scale approach. In the BP-Dock method, we mimic the nature of binding-induced events as a first-order approximation by perturbing the residues along the protein chain with a small Brownian kick one at a time. The response fluctuation profile of the chain upon these perturbations is computed using the p

SUBMITTER: Bolia A 

PROVIDER: S-EPMC4857727 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature