title: Blind Pose Prediction, Scoring, and Affinity Ranking of the CSAR 2014 Dataset.
abstract: The 2014 CSAR Benchmark Exercise was focused on three protein targets: coagulation factor Xa, spleen tyrosine kinase, and bacterial tRNA methyltransferase. Our protocol involved a preliminary analysis of the structural information available in the Protein Data Bank for the protein targets, which allowed the identification of the most appropriate docking software and scoring functions to be used for the rescoring of several docking conformations datasets, as well as for pose prediction and affinity ranking. The two key points of this study were (i) the prior evaluation of molecular modeling tools that are most adapted for each target and (ii) the increased search efficiency during the docking process to better explore the conformational space of big and flexible ligands.
authors.affiliation: Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT , 91198 Gif-sur-Yvette, France.|Department of Nephrology and Dialysis, AP-HP, Tenon Hospital, INSERM UMR_S 1155 , 75020 Paris, France.
authors.forename: Virginie Y
authors.initials: VY
authors.lastname: Martiny
authors.affiliation: Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT , 91198 Gif-sur-Yvette, France.
authors.forename: François
authors.initials: F
authors.lastname: Martz
authors.affiliation: Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT , 91198 Gif-sur-Yvette, France.
authors.forename: Edithe
authors.initials: E
authors.lastname: Selwa
authors.affiliation: Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT , 91198 Gif-sur-Yvette, France.
authors.forename: Bogdan I
authors.initials: BI
authors.lastname: Iorga
mesh_terms: D019985:Benchmarking; D030562:Databases, Protein; D015951:Factor Xa / Q000737:chemistry / Q000378:metabolism; D062105:Molecular Docking Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D000072377:Syk Kinase / Q000737:chemistry / Q000378:metabolism; D012359:tRNA Methyltransferases / Q000737:chemistry / Q000378:metabolism
chemical_list: D011506:Proteins; D012359:tRNA Methyltransferases; D000072377:Syk Kinase; D015951:Factor Xa