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Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program

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Computational Peptidology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1268))

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Abstract

This chapter provides the background theory and a practical protocol for performing Brownian dynamics simulation of peptides. Brownian dynamics simulation represents a complementary approach to Monte Carlo and molecular dynamics methods. Unlike Monte Carlo methods, it could provide dynamical information in a timescale longer than the momentum relaxation time. On the other hand, it is faster than molecular dynamics by approximating the solvent by a continuum and by operating in the over-damped limit. This chapter introduces the use of the University of Houston Brownian Dynamics (UHBD) program [1, 2] to perform Brownian dynamics simulation on peptides.

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Author information

Authors and Affiliations

  1. Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA

    Tongye Shen

  2. Department of Chemistry and Biochemistry, University of Missouri St Louis, St Louis, MO, 63121, USA

    Chung F. Wong

Authors
  1. Tongye Shen
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  2. Chung F. Wong
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Corresponding author

Correspondence to Chung F. Wong .

Editor information

Editors and Affiliations

  1. Center of Bioinformatics (COBI), School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China

    Peng Zhou

  2. Center of Bioinformatics (COBI), School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China

    Jian Huang

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Shen, T., Wong, C.F. (2015). Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program. In: Zhou, P., Huang, J. (eds) Computational Peptidology. Methods in Molecular Biology, vol 1268. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2285-7_5

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  • DOI: https://doi.org/10.1007/978-1-4939-2285-7_5

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2284-0

  • Online ISBN: 978-1-4939-2285-7

  • eBook Packages: Springer Protocols

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