title: Application of Hidden Markov Models in Biomolecular Simulations.
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.
authors.affiliation: Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Shukla
authors.affiliation: Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: Zahra
authors.initials: Z
authors.lastname: Shamsi
authors.affiliation: Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Moffett
authors.affiliation: Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: Balaji
authors.initials: B
authors.lastname: Selvam
authors.affiliation: Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. diwakar@illinois.edu.|Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. diwakar@illinois.edu.|National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. diwakar@illinois.edu.|Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. diwakar@illinois.edu.
authors.forename: Diwakar
authors.initials: D
authors.lastname: Shukla
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D030562:Databases, Protein; D004744:Enkephalin, Methionine / Q000737:chemistry*; D006801:Humans; D008390:Markov Chains; D010446:Peptide Fragments / Q000737:chemistry*
chemical_list: D010446:Peptide Fragments; D004744:Enkephalin, Methionine
keywords: Hidden Markov models; Markov state models; Molecular dynamics; Protein conformational change; Protein dynamics