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Application of Hidden Markov Models in Biomolecular Simulations

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Hidden Markov Models

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1552))

Abstract

Hidden Markov models (HMMs) provide a framework to analyze large trajectories of biomolecular simulation datasets. HMMs decompose the conformational space of a biological molecule into finite number of states that interconvert among each other with certain rates. HMMs simplify long timescale trajectories for human comprehension, and allow comparison of simulations with experimental data. In this chapter, we provide an overview of building HMMs for analyzing bimolecular simulation datasets. We demonstrate the procedure for building a Hidden Markov model for Met-enkephalin peptide simulation dataset and compare the timescales of the process.

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Author information

Authors and Affiliations

  1. Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Saurabh Shukla, Zahra Shamsi, Balaji Selvam & Diwakar Shukla

  2. Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Alexander S. Moffett & Diwakar Shukla

  3. National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Diwakar Shukla

  4. Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Diwakar Shukla

Authors
  1. Saurabh Shukla
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  2. Zahra Shamsi
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  3. Alexander S. Moffett
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  4. Balaji Selvam
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  5. Diwakar Shukla
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Corresponding author

Correspondence to Diwakar Shukla .

Editor information

Editors and Affiliations

  1. University of Leeds School of Molecular and Cellular Biology, Leeds, United Kingdom

    David R. Westhead

  2. University of Leeds School of Cellular and Molecular Biology, Leeds, United Kingdom

    M. S. Vijayabaskar

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Shukla, S., Shamsi, Z., Moffett, A.S., Selvam, B., Shukla, D. (2017). Application of Hidden Markov Models in Biomolecular Simulations. In: Westhead, D., Vijayabaskar, M. (eds) Hidden Markov Models. Methods in Molecular Biology, vol 1552. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6753-7_3

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  • DOI: https://doi.org/10.1007/978-1-4939-6753-7_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6751-3

  • Online ISBN: 978-1-4939-6753-7

  • eBook Packages: Springer Protocols

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