Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

: Docking is one of the most commonly used techniques in drug design. It is used for both identifying correct poses of a ligand in the binding site of a protein as well as for the estimation of the strength of protein– ligand interaction. Because millions of compounds must be screened, before a suitable target for biological testing can be identified, all calculations should be done in a reasonable time frame. Thus, all programs currently in use exploit empirically based algorithms, avoiding systematic search of the conformational space. Similarly, the scoring is done using simple equations, which makes it possible to speed up the entire process. Therefore, docking results have to be verified by subsequent in vitro studies. The purpose of our work was to evaluate seven popular docking programs (Surflex, LigandFit, Glide, GOLD, FlexX, eHiTS, and AutoDock) on the extensive dataset composed of 1300 protein–ligands complexes from PDBbind 2007 database, where experimentally measured ...

• Type: Journal
• Year: 2011
• Where: JCC
• Authors: Dariusz Plewczynski, Michal Lazniewski, Rafal Augustyniak, Krzysztof Ginalski
• Keywords: Comput Chem, JCC 2011, Ligands Complexes, Protein Families