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Virtual Ligand Screening Against Comparative Protein Structure Models

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Computational Drug Discovery and Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 819))

Abstract

Virtual ligand screening uses computation to discover new ligands of a protein by screening one or more of its structural models against a database of potential ligands. Comparative protein structure modeling extends the applicability of virtual screening beyond the atomic structures determined by X-ray crystallography or NMR spectroscopy. Here, we describe an integrated modeling and docking protocol, combining comparative modeling by MODELLER and virtual ligand screening by DOCK.

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Acknowledgement

This article is partially based on the MODELLER manual, the DOCK 3.5 manual, and the “DISI” wiki pages (http://wiki.bkslab.org). We also acknowledge funds from Sandler Family Supporting Foundation and National Institutes of Health (R01 GM54762 to AS; R01 GM71896 to BKS and JJI; P01 GM71790 and U54 GM71790 to AS and BKS). We are also grateful to Ron Conway, Mike Homer, Hewlett-Packard, IBM, NetApp, and Intel for hardware gifts.

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Authors and Affiliations

  1. Departments of Bioengineering & Therapeutic Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA

    Hao Fan

  2. Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA

    John J. Irwin

  3. Departments of Bioengineering & Therapeutic Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA

    Andrej Sali

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  2. John J. Irwin
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  3. Andrej Sali
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Corresponding authors

Correspondence to Hao Fan or Andrej Sali .

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Editors and Affiliations

  1. University of Utah, 30 South 2000 East Rm 307, Salt Lake City, 84112-5820, California, USA

    Riccardo Baron

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© 2012 Springer Science+Business Media, LLC

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Fan, H., Irwin, J.J., Sali, A. (2012). Virtual Ligand Screening Against Comparative Protein Structure Models. In: Baron, R. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 819. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-465-0_8

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  • DOI: https://doi.org/10.1007/978-1-61779-465-0_8

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-464-3

  • Online ISBN: 978-1-61779-465-0

  • eBook Packages: Springer Protocols

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