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Molecular Dynamics Simulation and Prediction of Druggable Binding Sites

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Computational Drug Discovery and Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1762))

Abstract

Binding site identification and druggability evaluation are two essential steps in structure-based drug design. A druggable binding site tends to have high binding affinity to drug-like molecules. Predicting such sites can have a significant impact on a drug design campaign. This chapter focuses on summarizing the different methods that are used to predict druggable binding sites. The chapter also discusses the importance of including protein flexibility in the search process and the use of molecular dynamics simulations to address this aspect. Case studies from the literature are also summarized and discussed. We hope that this chapter would provide an overview on the different methods employed in binding site identification evaluation.

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Authors and Affiliations

  1. Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada

    Tianhua Feng & Khaled Barakat

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  1. Tianhua Feng
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  2. Khaled Barakat
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Correspondence to Khaled Barakat .

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Editors and Affiliations

  1. Department of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, KA, India

    Mohini Gore

  2. Department of Biotechnology, Shivaji University, Kolhapur, MH, India

    Umesh B. Jagtap

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Feng, T., Barakat, K. (2018). Molecular Dynamics Simulation and Prediction of Druggable Binding Sites. In: Gore, M., Jagtap, U. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 1762. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7756-7_6

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  • DOI: https://doi.org/10.1007/978-1-4939-7756-7_6

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7755-0

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