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Exploring the energy landscapes of protein folding simulations with Bayesian computation

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Burkoff, Nikolas S., Várnai, Csilla, Wells, Stephen A. and Wild, David L. (2012) Exploring the energy landscapes of protein folding simulations with Bayesian computation. Biophysical Journal, Vol.102 (No.4). pp. 878-886. doi:10.1016/j.bpj.2011.12.053

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Official URL: http://dx.doi.org/10.1016/j.bpj.2011.12.053

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Abstract

Nested sampling is a Bayesian sampling technique developed to explore probability distributions localized in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence (marginal likelihood) of the model. The nested sampling algorithm also provides an efficient way to calculate free energies and the expectation value of thermodynamic observables at any temperature, through a simple post processing of the output. Previous applications of the algorithm have yielded large efficiency gains over other sampling techniques, including parallel tempering. In this article, we describe a parallel implementation of the nested sampling algorithm and its application to the problem of protein folding in a Gō-like force field of empirical potentials that were designed to stabilize secondary structure elements in room-temperature simulations. We demonstrate the method by conducting folding simulations on a number of small proteins that are commonly used for testing protein-folding procedures. A topological analysis of the posterior samples is performed to produce energy landscape charts, which give a high-level description of the potential energy surface for the protein folding simulations. These charts provide qualitative insights into both the folding process and the nature of the model and force field used.

Item Type: Journal Article
Divisions: Faculty of Science > Physics
Faculty of Science > Centre for Systems Biology
Journal or Publication Title: Biophysical Journal
Publisher: Biophysical Society
ISSN: 0006-3495
Official Date: 22 February 2012
Dates:
DateEvent
22 February 2012Published
Volume: Vol.102
Number: No.4
Page Range: pp. 878-886
DOI: 10.1016/j.bpj.2011.12.053
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access

Data sourced from Thomson Reuters' Web of Knowledge

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