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On Setting Up and Assessing Docking Simulations for Virtual Screening

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Rational Drug Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 928))

Abstract

Small molecule docking and virtual screening of candidate compounds have become an integral part of drug discovery pipelines, complementing and streamlining experimental efforts in that regard. In this chapter, we describe specific software packages and protocols that can be used to efficiently set up a computational screening using a library of compounds and a docking program. We also discuss consensus- and clustering-based approaches that can be used to assess the results, and potentially re-rank the hits. While docking programs share many common features, they may require tailored implementation of virtual screening pipelines for specific computing platforms. Here, we primarily focus on solutions for several public domain packages that are widely used in the context of drug development.

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Acknowledgments

This work was supported in part by NIH grants A1055649, UL1RR026314, and P01HD013021. Computational resources were made available by Cincinnati Childrens Hospital Research Foundation and University of Cincinnati College of Medicine.

Author information

Authors and Affiliations

  1. Biomedical Informatics, Children’s Hospital Research Foundation, Cincinnati, OH, USA

    Jacek Biesiada & Jaroslaw Meller

  2. Division of Management and Informatics, Technical University of Silesia, Katowice, Poland

    Jacek Biesiada

  3. Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA

    Aleksey Porollo & Jaroslaw Meller

  4. Department of Informatics, Nicholas Copernicus University, Torun, Poland

    Jaroslaw Meller

Authors
  1. Jacek Biesiada
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  2. Aleksey Porollo
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  3. Jaroslaw Meller
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Corresponding author

Correspondence to Jaroslaw Meller .

Editor information

Editors and Affiliations

  1. Research Foundation, Div. Experimental Hematology, Cincinnati Children's Hospital, Burnet Ave. 3333, Cincinnati, 45229, Ohio, USA

    Yi Zheng

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Biesiada, J., Porollo, A., Meller, J. (2012). On Setting Up and Assessing Docking Simulations for Virtual Screening. In: Zheng, Y. (eds) Rational Drug Design. Methods in Molecular Biology, vol 928. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-008-3_1

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  • DOI: https://doi.org/10.1007/978-1-62703-008-3_1

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-007-6

  • Online ISBN: 978-1-62703-008-3

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