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

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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.

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Acknowledgments

The authors thank Dr. Eva Mª Priego and Dr. Alberto Gómez for testing the application and valuable comments, as well as the rest of members of the Bioinformatics Unit at CBMSO and the Molecular Modeling group at UAH for encouragement and fruitful discussions. This work was supported by grants from Ministerio de Ciencia e Innovación (MICINN) BIO2008-04384 (to A. M.) and SAF2009-13914-C02-02 (to F. G.), and Comunidad Autónoma de Madrid (CAM) S-BIO-0214-2006. A. M. acknowledges CAM for financial support through the AMAROUTO program to the Fundación Severo Ochoa, R. G. -R. thanks MICINN for a contract from “Programa de Personal Técnico y de Apoyo 2008”, and A. C. thanks Ministerio de Educación for the FPU grant AP2009-0203. We are grateful to OpenEye Scientific Software, Inc. for providing us with an academic license for their software. The technical support and advice from the Bioinformatics Facility at CBMSO is gratefully acknowledged, as well as the computer resources, technical expertise and assistance provided by the Barcelona Supercomputing Center—Centro Nacional de Supercomputación.

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Authors and Affiliations

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

    Álvaro Cortés Cabrera & Federico Gago

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

    Álvaro Cortés Cabrera, Rubén Gil-Redondo, Almudena Perona & Antonio Morreale

Authors
  1. Álvaro Cortés Cabrera
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  2. Rubén Gil-Redondo
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  3. Almudena Perona
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  4. Federico Gago
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  5. Antonio Morreale
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Corresponding author

Correspondence to Antonio Morreale.

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Cabrera, Á.C., Gil-Redondo, R., Perona, A. et al. VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface. J Comput Aided Mol Des 25, 813–824 (2011). https://doi.org/10.1007/s10822-011-9465-6

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