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 (email@example.com) for further information.
1Unidad de Bioinformática. Centro de Biología Molecular Severo Ochoa (CSIC-UAM). c/ Nicolás Cabrera 1. Campus de Cantoblanco. Madrid 28049. Spain.
2Departamento 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.
3Department of Chemistry. Imperial College London. South Kensington. London SW7 2AZ. United Kingdom.
# Deceased on May 5, 2008.