Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints.

ABSTRACT: The rapidly growing number of theoretically predicted protein structures requires robust methods that can utilize low-quality receptor structures as targets for ligand docking. Typically, docking accuracy falls off dramatically when apo or modeled receptors are used in docking experiments. Low-resolution ligand docking techniques have been developed to deal with structural inaccuracies in predicted receptor models. In this spirit, we describe the development and optimization of a knowledge-based potential implemented in Q-Dock, a low-resolution flexible ligand docking approach. Self-docking experiments using crystal structures reveals satisfactory accuracy, comparable with all-atom docking. All-atom models reconstructed from Q-Dock's low-resolution models can be further refined by even a s

SUBMITTER: Brylinski M 

PROVIDER: S-EPMC2726574 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature