title: Reranking docking poses using molecular simulations and approximate free energy methods.
abstract: Fast and accurate identification of active compounds is essential for effective use of virtual screening workflows. Here, we have compared the ligand-ranking efficiency of the linear interaction energy (LIE) method against standard docking approaches. Using a trypsin set of 1549 compounds, we performed 12,250 molecular dynamics simulations. The LIE method proved effective but did not yield results significantly better than those obtained with docking codes. The entire database of simulations is released.
authors.affiliation: Dipartimento di Farmacia, Università degli Studi di Salerno , Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.
authors.forename: G
authors.initials: G
authors.lastname: Lauro
authors.forename: N
authors.initials: N
authors.lastname: Ferruz
authors.forename: S
authors.initials: S
authors.lastname: Fulle
authors.forename: M J
authors.initials: MJ
authors.lastname: Harvey
authors.forename: P W
authors.initials: PW
authors.lastname: Finn
authors.forename: G
authors.initials: G
authors.lastname: De Fabritiis
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D057166:High-Throughput Screening Assays; D008024:Ligands; D062105:Molecular Docking Simulation; D011485:Protein Binding; D012372:ROC Curve; D013816:Thermodynamics; D014357:Trypsin / Q000737:chemistry*; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D014357:Trypsin