The Library
Exploring the energy landscapes of protein folding simulations with Bayesian computation
Tools
Tools
Tools
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
Research output not available from this repository, contact author.
Official URL: http://dx.doi.org/10.1016/j.bpj.2011.12.053
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: |
|
||||
| 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
Request changes or add full text files to a record
Repository staff actions (login required)
 |
View Item |
