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Structure-Based Virtual Screening for Novel Ligands

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Protein-Ligand Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1008))

Abstract

Computational searches for novel ligands for a given protein binding site have become ubiquitous in the pharmaceutical industry, and are potentially equally useful in helping identify small-molecule tools for biology. Here we describe the steps needed to carry out a high-throughput docking (HTD) or three-dimensional (3D) pharmacophore virtual screen starting with a model of the target protein’s structure. The advice given is, in most cases, software independent but some tips are provided which apply only to certain popular programs. Useful work can be carried out using free programs on a modest workstation. Of course, any resultant “hits” remain in the virtual world until they are experimentally tested.

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Acknowledgments

Our thanks to Professor Tom Blundell, Dr. Sachin Surade, Sean Boyle, and Gengshi Chen for the use of Fig. 1.

Author information

Authors and Affiliations

  1. Department of Medicinal Chemistry, UCB Pharma, Slough, UK

    William R. Pitt, Mark D. Calmiano, Boris Kroeplien, Richard D. Taylor, James P. Turner & Michael A. King

Authors
  1. William R. Pitt
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  2. Mark D. Calmiano
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  3. Boris Kroeplien
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  4. Richard D. Taylor
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  5. James P. Turner
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  6. Michael A. King
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Editor information

Editors and Affiliations

  1. Birbeck, University of London, ISMB Biophysics Centre, Institute of Str, Malet Street, London, WC1E 7HX, United Kingdom

    Mark A. Williams

  2. Birkbeck, University of London, School of Crystallography, ISMB Biophysics Centre, Institute of Str, Malet Street, London, WC1E 7HX, United Kingdom

    Tina Daviter

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Pitt, W.R., Calmiano, M.D., Kroeplien, B., Taylor, R.D., Turner, J.P., King, M.A. (2013). Structure-Based Virtual Screening for Novel Ligands. In: Williams, M., Daviter, T. (eds) Protein-Ligand Interactions. Methods in Molecular Biology, vol 1008. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-398-5_19

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  • DOI: https://doi.org/10.1007/978-1-62703-398-5_19

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-397-8

  • Online ISBN: 978-1-62703-398-5

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