Journal of Computer-Aided Molecular Design

, Volume 23, Issue 3, pp 171–184

VSDMIP: virtual screening data management on an integrated platform

  • Rubén Gil-Redondo
  • Jorge Estrada
  • Antonio Morreale
  • Fernando Herranz
  • Javier Sancho
  • Ángel R. Ortiz
Article

DOI: 10.1007/s10822-008-9249-9

Cite this article as:
Gil-Redondo, R., Estrada, J., Morreale, A. et al. J Comput Aided Mol Des (2009) 23: 171. doi:10.1007/s10822-008-9249-9

Abstract

A novel software (VSDMIP) for the virtual screening (VS) of chemical libraries integrated within a MySQL relational database is presented. 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. To validate the usefulness of VSDMIP as an automated tool for carrying out VS several experiments were run on six protein targets (acetylcholinesterase, cyclin-dependent kinase 2, coagulation factor Xa, estrogen receptor alpha, p38 MAP kinase, and neuraminidase) using nine binary (actives/inactive) test sets. The performance of several VS configurations was evaluated by means of enrichment factors and receiver operating characteristic plots.

Keywords

Docking Virtual screening Drug design Database Platform 

Abbreviations

AChE

Acetylcholinesterase

fXa

Coagulation factor Xa

CDK2

Cyclic dependant kinase 2

Era

Estrogen receptor a

p38MAP

MAP Kinase P38

VS

Virtual Screening

EF

Enrichment Factor

ROC

Receiver Operating Characteristic

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Rubén Gil-Redondo
    • 1
  • Jorge Estrada
    • 2
  • Antonio Morreale
    • 1
  • Fernando Herranz
    • 1
  • Javier Sancho
    • 2
  • Ángel R. Ortiz
    • 1
  1. 1.Unidad De Bioinformática, Centro De Biología Molecular Severo Ochoa (CSIC-UAM)MadridSpain
  2. 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 12Universidad de ZaragozaZaragozaSpain

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