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Computing Ensembles of Transitions with Molecular Dynamics Simulations

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Molecular Modeling of Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1215))

Abstract

A molecular understanding of conformational change is important for connecting structure and function. Without the ability to sample on the meaningful large-scale conformational changes, the ability to infer biological function and to understand the effect of mutations and changes in environment is not possible. Our Dynamic Importance Sampling method (DIMS), part of the CHARMM simulation package, is a method that enables sampling over ensembles of transition intermediates. This chapter outlines the context for the method and the usage within the program.

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Authors and Affiliations

  1. Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews, Room 3143, Urbana, IL, 61801, USA

    Juan R. Perilla

  2. Department of Physiology, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD, 21205, USA

    Thomas B. Woolf

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  1. Juan R. Perilla
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  2. Thomas B. Woolf
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Correspondence to Thomas B. Woolf .

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Editors and Affiliations

  1. University of Hertfordshire, Hatfield, Hertfordshire, United Kingdom

    Andreas Kukol

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Perilla, J.R., Woolf, T.B. (2015). Computing Ensembles of Transitions with Molecular Dynamics Simulations. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods in Molecular Biology, vol 1215. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1465-4_11

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  • DOI: https://doi.org/10.1007/978-1-4939-1465-4_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1464-7

  • Online ISBN: 978-1-4939-1465-4

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