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Rational Drug Design pp 67–88Cite as

Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1824))

Abstract

Main goal in drug discovery is the identification of drug-like compounds capable to modulate specific biological targets. Thus, the prediction of reliable binding poses of candidate ligands, through molecular docking simulations, represents a key step to be pursued in structure-based drug design (SBDD). Since the increasing number of resolved three-dimensional ligand-protein structures, together with the expansion of computational power and software development, the comprehensive and systematic use of experimental data can be proficiently employed to validate the docking performance. This allows to select and refine the protocol to adopt when predicting the binding pose of trial compounds in a target. Given the availability of multiple docking software, a comparative docking assessment in an early research stage represents a must-use step to minimize fails in molecular modeling. This chapter describes how to perform a docking assessment, using freely available tools, in a semiautomated fashion.

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Acknowledgments

F.B. thanks Prof. Garland R. Marshall (Washington University School of Medicine in St. Louis, MO) for supporting and funding the design and development of the Clusterizer-DockAccessor protocol; Dr. Chris M. W. Ho (Drug Design Methodologies, LLC, St. Louis, MO) and Ms. Mariama Jaiteh (Uppsala University, Uppsala, Sweden) for providing insightful comments.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA

    Flavio Ballante

  2. Department of Cell and Molecular Biology, Uppsala Biomedicinska Centrum BMC, Uppsala University, Uppsala, Sweden

    Flavio Ballante

Authors
  1. Flavio Ballante
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Correspondence to Flavio Ballante .

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Editors and Affiliations

  1. Division of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece

    Thomas Mavromoustakos

  2. Division of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece

    Tahsin F. Kellici

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Ballante, F. (2018). Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection. In: Mavromoustakos, T., Kellici, T. (eds) Rational Drug Design. Methods in Molecular Biology, vol 1824. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8630-9_5

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  • DOI: https://doi.org/10.1007/978-1-4939-8630-9_5

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8629-3

  • Online ISBN: 978-1-4939-8630-9

  • eBook Packages: Springer Protocols

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