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Journal of Computer-Aided Molecular Design

, Volume 23, Issue 3, pp 171–184 | Cite as

VSDMIP: virtual screening data management on an integrated platform

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

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

Notes

Acknowledgements

Work at the CBM-SO was partially supported by a grant from “Comunidad de Madrid” thorough BIPEDD project (SBIO-0214–2006) and from “Ministerio de Educación y Ciencia” (BIO2005–0576). J.S. and J.E. were funded by grants BFU2007–61476/BMC (MEC, Spain) and PM076/2006 (DGA, Spain). J.E.’s research stage at CBM “Severo Ochoa” was funded by grants DGA (CONSI + D)/CAI (Spain) and FPU (MEC, Spain). J.E. is recepient of an FPU grant (MEC, Spain). J.E. thanks Alejandra Leo-Macías for help in using the MODELLER software. A.M. and R.G.-R. thank David Abia and Rubén Muñoz for technical support. We also acknowledge the generous allocation of computer time at the Barcelona Supercomputing Center. This work would not have been possible without the encouraging help of Ángel R. Ortiz, to whose memory this article is dedicated.

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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Rubén Gil-Redondo
    • 1
  • Jorge Estrada
    • 2
  • Antonio Morreale
    • 1
    Email author
  • 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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