title: Predicting Binding Poses and Affinities in the CSAR 2013-2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential.
abstract: The 2013-2014 CSAR docking exercise was the opportunity to assess the performance of the novel knowledge-based potential we are developing, named Convex-PL. The data used to derive the potential consists only of structural information from protein-ligand interfaces found in the PDBBind database. As expected, our potential proved to be very efficient in the near-native pose detection exercises, where we correctly predicted two near-native poses in the 2013 exercise and also ranked 22 near-native poses first and 2 second in the 2014 exercise. Somewhat more surprisingly, we obtained a fair performance in some of the CSAR affinity ranking exercises, where the Spearman correlation coefficients between our predictions and the experiments are greater than 0.5 for several protein-ligand sets. Nonetheless, affinity prediction exercises turned out to be a challenge, and significant progress in the development of our method is needed before we can successfully predict binding constants.
authors.affiliation: University Grenoble Alpes, LJK , F-38000 Grenoble, France.|CNRS, LJK , F-38000 Grenoble, France.|Inria , F-38000 Grenoble, France.
authors.forename: Sergei
authors.initials: S
authors.lastname: Grudinin
authors.affiliation: University Grenoble Alpes, LJK , F-38000 Grenoble, France.|CNRS, LJK , F-38000 Grenoble, France.|Inria , F-38000 Grenoble, France.|Moscow Institute of Physics and Technology , Dolgoprudniy, 141700, Russia.
authors.forename: Petr
authors.initials: P
authors.lastname: Popov
authors.affiliation: University Grenoble Alpes, LJK , F-38000 Grenoble, France.|CNRS, LJK , F-38000 Grenoble, France.|Inria , F-38000 Grenoble, France.
authors.forename: Emilie
authors.initials: E
authors.lastname: Neveu
authors.affiliation: University Grenoble Alpes, LJK , F-38000 Grenoble, France.|CNRS, LJK , F-38000 Grenoble, France.|Inria , F-38000 Grenoble, France.|Moscow Institute of Physics and Technology , Dolgoprudniy, 141700, Russia.
authors.forename: Georgy
authors.initials: G
authors.lastname: Cheremovskiy
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D055808:Drug Discovery; D008024:Ligands; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D008024:Ligands; D011506:Proteins