title: A New, Improved Hybrid Scoring Function for Molecular Docking and Scoring Based on AutoDock and AutoDock Vina.
abstract: Automated docking is one of the most important tools for structure-based drug design that allows prediction of ligand binding poses and also provides an estimate of how well small molecules fit in the binding site of a protein. A new scoring function based on AutoDock and AutoDock Vina has been introduced. The new hybrid scoring function is a linear combination of the two scoring function components derived from a multiple linear regression fitting procedure. The scoring function was built on a training set of 2412 protein-ligand complexes from pdbbind database (www.pdbbind.org.cn, version 2012). A test set of 313 complexes that appeared in the 2013 version was used for validation purposes. The new hybrid scoring function performed better than the original functions, both on training and test sets of protein-ligand complexes, as measured by the non-parametric Pearson correlation coefficient, R, mean absolute error (MAE), and root-mean-square error (RMSE) between the experimental binding affinities and the docking scores. The function also gave one of the best results among more than 20 scoring functions tested on the core set of the pdbbind database. The new AutoDock hybrid scoring function will be implemented in modified version of AutoDock.
authors.affiliation: Department of Bioorganic Mechanisms, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, 1 Murmanska Street-94, Kyiv, 02660, Ukraine.
authors.forename: Vsevolod Yu
authors.initials: VY
authors.lastname: Tanchuk
authors.affiliation: Department of Bioorganic Mechanisms, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, 1 Murmanska Street-94, Kyiv, 02660, Ukraine.
authors.forename: Volodymyr O
authors.initials: VO
authors.lastname: Tanin
authors.affiliation: Department of Bioorganic Mechanisms, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, 1 Murmanska Street-94, Kyiv, 02660, Ukraine.
authors.forename: Andriy I
authors.initials: AI
authors.lastname: Vovk
authors.affiliation: Drug Discovery Program, Ontario Institute for Cancer Research (OICR), 661 University Avenue, Suite 510, Toronto, ON, Canada, M5G 0A3.|Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON, Canada, M5S 3M2.
authors.forename: Gennady
authors.initials: G
authors.lastname: Poda
mesh_terms: D015195:Drug Design; D062105:Molecular Docking Simulation
keywords: AutoDock; AutoDock Vina; hybrid scoring function; molecular docking; scoring; virtual screening