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VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface

Alvaro Cortes Cabrera1,2, Ruben Gil-Redondo2, Almudena Perona2, Federico Gago1 and Antonio Morreale2*

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.

*Please contact Antonio Morreale (amorreale@cbm.uam.es) for further information.

1Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain

2 Unidad de Bioinformática. Centro de Biología Molecular Severo Ochoa (CSIC-UAM). c/ Nicolás Cabrera 1. Campus de Cantoblanco. Madrid 28049. Spain.

VSDMIP: Virtual Screening Data Management on an Integrated Platform

Rubén Gil-Redondo1, Jorge Estrada2, Antonio Morreale*1, Fernando Herranz3, Javier Sancho2,and Ángel R. Ortiz#1

We present here a novel software (VSDMIP) for the virtual screening (VS) of chemical libraries integrated within a MySQL relational database. Two main features make VSDMIP clearly distinguishable from other existing computational tools: (i) its database, which stores not only ligand information but also the results from every step in the VS process, and (ii) its modular and pluggable architecture, which allows customization of the VS stages (such as the programs used for conformer generation or docking), through the definition of a detailed workflow employing user-configurable XML files. VSDMIP, therefore, facilitates the storage and retrieval of VS results, easily adapts to the specific requirements of each method and tool used in the experiments, and allows the comparison of different VS methodologies.

The article describing the platform has been published in Journal of Computer Aided Molecular Design and it has doi:10.1007/s10822-008-9249-9. The platform has been prepared as a bundled package to be distributed to the scientific community upon request from the authors. In brief, all the programs implemented in the platform (except those that need to be purchased, by a modest prize, as CORINA or DelPhi) are either free (MOPAC, DOCK, FRED, AutoDock) or are released under a scientific/academic non-profit and non-commercial license as ALFA, CGRID, CDOCK, and ISM. Also the scripts to create the database structure as well as XML configuration files are provided.

*Please contact Antonio Morreale (amorreale@cbm.uam.es) for further information.

1 Unidad de Bioinformática. Centro de Biología Molecular Severo Ochoa (CSIC-UAM). c/ Nicolás Cabrera 1. Campus de Cantoblanco. Madrid 28049. Spain.

2 Departamento de Bioquímica y Biología Molecular y Celular. >Facultad de Ciencias and BIFI –Instituto de Biocomputación y Física de Sistemas Complejos. c/ Pedro Cerbuna 12. Universidad de Zaragoza. 50009 Zaragoza. Spain.

3 Department of Chemistry. Imperial College London. South Kensington. London SW7 2AZ. United Kingdom.

# Deceased on May 5, 2008.

  • VSDMIP is a platform for virtual screening (VS) of chemical libraries, integrated within a MySQL relational database. Read more ....
  • The software is freely distributed for academic and research purposes upon request to the authors. Contact Antonio Morreale (amorreale@cbm.uam.es) for details.
  • Reference : Gil-Redondo, R.; Estrada, J.; Morreale, A.; Herranz, F.; Sancho, J.; Ortiz, A.R. J Comput -Aided Mol Design (submitted )

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