title: VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface.
abstract: A graphical user interface (GUI) for our previously published virtual screening (VS) and data management platform VSDMIP (Gil-Redondo et al. J Comput Aided Mol Design, 23:171-184, 2009) that has been developed as a plugin for the popular molecular visualization program PyMOL is presented. In addition, a ligand-based VS module (LBVS) has been implemented that complements the already existing structure-based VS (SBVS) module and can be used in those cases where the receptor's 3D structure is not known or for pre-filtering purposes. This updated version of VSDMIP is placed in the context of similar available software and its LBVS and SBVS capabilities are tested here on a reduced set of the Directory of Useful Decoys database. Comparison of results from both approaches confirms the trend found in previous studies that LBVS outperforms SBVS. We also show that by combining LBVS and SBVS, and using a cluster of ~100 modern processors, it is possible to perform complete VS studies of several million molecules in less than a month. As the main processes in VSDMIP are 100% scalable, more powerful processors and larger clusters would notably decrease this time span. The plugin is distributed under an academic license upon request from the authors.
authors.affiliation: Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain.
authors.forename: Álvaro Cortés
authors.initials: ÁC
authors.lastname: Cabrera
authors.forename: Rubén
authors.initials: R
authors.lastname: Gil-Redondo
authors.forename: Almudena
authors.initials: A
authors.lastname: Perona
authors.forename: Federico
authors.initials: F
authors.lastname: Gago
authors.forename: Antonio
authors.initials: A
authors.lastname: Morreale
mesh_terms: D017076:Computer-Aided Design; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D012984:Software; D014584:User-Computer Interface
chemical_list: D008024:Ligands