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Molecular Dynamics

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Computational Toxicology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 929))

Abstract

Molecular dynamics (MD) simulation holds the promise of revealing the mechanisms of biological processes in their ultimate detail. It is carried out by computing the interaction forces acting on each atom and then propagating the velocities and positions of the atoms by numerical integration of Newton’s equations of motion. In this review, we present an overview of how the MD simulation can be conducted to address computational toxicity problems. The study cases will cover a standard MD simulation performed to investigate the overall flexibility of a cytochrome P450 (CYP) enzyme and a set of more advanced MD simulations to examine the barrier to ion conduction in a human α7 nicotinic acetylcholine receptor (nAChR).

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Authors and Affiliations

  1. Oak Ridge National Laboratory, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA

    Xiaolin Cheng

  2. Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA

    Xiaolin Cheng

  3. Department of Chemistry, Georgia State University, Atlanta, GA, USA

    Ivaylo Ivanov

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  1. Xiaolin Cheng
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  2. Ivaylo Ivanov
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Correspondence to Xiaolin Cheng .

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Editors and Affiliations

  1. School of Biomedical Engineering, Chemical & Biological Engineering, Colorado State University, Campus Delivery 1370, Fort Collins, 80523-1370, Colorado, USA

    Brad Reisfeld

  2. , Chemical & Biological Engineering, Colorado State University, Campus Delivery 1370, Fort Collins, 80523-1370, Colorado, USA

    Arthur N. Mayeno

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Cheng, X., Ivanov, I. (2012). Molecular Dynamics. In: Reisfeld, B., Mayeno, A. (eds) Computational Toxicology. Methods in Molecular Biology, vol 929. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-050-2_11

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  • DOI: https://doi.org/10.1007/978-1-62703-050-2_11

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