title: Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets.
abstract: The D3R Grand Challenge 2015 was focused on two protein targets: Heat Shock Protein 90 (HSP90) and Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4). We used a protocol involving a preliminary analysis of the available data in PDB and PubChem BioAssay, and then a docking/scoring step using more computationally demanding parameters that were required to provide more reliable predictions. We could evidence that different docking software and scoring functions can behave differently on individual ligand datasets, and that the flexibility of specific binding site residues is a crucial element to provide good predictions.
authors.affiliation: Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT, Université Paris-Saclay, 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, Université Paris-Saclay, 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, Université Paris-Saclay, 91198, Gif-sur-Yvette, France. bogdan.iorga@cnrs.fr.
authors.forename: Bogdan I
authors.initials: BI
authors.lastname: Iorga
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D030562:Databases, Protein; D015195:Drug Design; D018841:HSP90 Heat-Shock Proteins / Q000737:chemistry*; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry*; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods*; D011485:Protein Binding; D011487:Protein Conformation; D017346:Protein Serine-Threonine Kinases / Q000737:chemistry*; D013329:Structure-Activity Relationship
chemical_list: D018841:HSP90 Heat-Shock Proteins; D047908:Intracellular Signaling Peptides and Proteins; D008024:Ligands; C117090:MAP4K4 protein, human; D017346:Protein Serine-Threonine Kinases
keywords: Autodock; D3R Grand Challenge 2015; Docking; Glide; Gold; HSP90; Heat Shock Protein 90; MAP4K4; Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4; Scoring function