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The Role and Application of In Silico Docking in Chemical Genomics Research

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Chemical Genomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 310))

Abstract

In silico docking techniques are being used to investigate the complementarity at the molecular level of a ligand and a protein target. As such, docking studies can be used to identify the structural features that are important for binding and for in silico screening efforts in which suitable binding partners can be identified. Here we describe a practical approach for setting up docking simulations using different docking programs. We also cover the analysis and rescoring of the obtained docking poses. Possible pitfalls in the docking studies are discussed and hints are provided to resolve commonly occurring problems.

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Author information

Authors and Affiliations

  1. Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research (LACDR), Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands

    Aldo Jongejan, Chris de Graaf, Nico P. E. Vermeulen, Rob Leurs & Iwan J. P. de Esch

Authors
  1. Aldo Jongejan
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  2. Chris de Graaf
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  3. Nico P. E. Vermeulen
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  4. Rob Leurs
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  5. Iwan J. P. de Esch
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Editors and Affiliations

  1. CamBP Ltd., Cambridge, UK

    Edward D. Zanders PhD

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© 2005 Humana Press Inc.

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Jongejan, A., de Graaf, C., Vermeulen, N.P.E., Leurs, R., de Esch, I.J.P. (2005). The Role and Application of In Silico Docking in Chemical Genomics Research. In: Zanders, E.D. (eds) Chemical Genomics. Methods in Molecular Biology™, vol 310. Humana Press. https://doi.org/10.1007/978-1-59259-948-6_5

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  • DOI: https://doi.org/10.1007/978-1-59259-948-6_5

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-399-2

  • Online ISBN: 978-1-59259-948-6

  • eBook Packages: Springer Protocols

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