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Molecular Dynamics Simulations of Protein–Drug Complexes: A Computational Protocol for Investigating the Interactions of Small-Molecule Therapeutics with Biological Targets and Biosensors

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Computational Drug Discovery and Design

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

Abstract

MD simulations provide a powerful tool for the investigation of protein–drug complexes. The following chapter uses the aryl acylamidase–acetaminophen system as an example to describe a general protocol for preparing and running simulations of protein–drug complexes, complete with a step-by-step tutorial. The described approach is broadly applicable toward the study of drug interactions in the context of both biological targets and biosensing enzymes.

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Acknowledgements

The authors acknowledge funding from the University of Delaware and the National Institutes of Health COBRE grant 5P30GM110758-04.

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA

    Jodi A. Hadden & Juan R. Perilla

Authors
  1. Jodi A. Hadden
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  2. Juan R. Perilla
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Corresponding author

Correspondence to Jodi A. Hadden .

Editor information

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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Hadden, J.A., Perilla, J.R. (2018). Molecular Dynamics Simulations of Protein–Drug Complexes: A Computational Protocol for Investigating the Interactions of Small-Molecule Therapeutics with Biological Targets and Biosensors. 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_13

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  • DOI: https://doi.org/10.1007/978-1-4939-7756-7_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7755-0

  • Online ISBN: 978-1-4939-7756-7

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