Toward prediction of functional protein pockets using blind docking and pocket search algorithms.

ABSTRACT: Location of functional binding pockets of bioactive ligands on protein molecules is essential in structural genomics and drug design projects. If the experimental determination of ligand-protein complex structures is complicated, blind docking (BD) and pocket search (PS) calculations can help in the prediction of atomic resolution binding mode and the location of the pocket of a ligand on the entire protein surface. Whereas the number of successful predictions by these methods is increasing even for the complicated cases of exosites or allosteric binding sites, their reliability has not been fully established. For a critical assessment of reliability, we use a set of ligand-protein complexes, which were found to be problematic in previous studies. The robustness of BD and PS methods is add

SUBMITTER: Hetenyi C 

PROVIDER: S-EPMC3125872 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature