PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure
作者： Wouter Boomsma , Jes Frellsen , Tim Harder , Sandro Bottaro , Kristoffer E. Johansson
DOI: 10.1002/JCC.23292
关键词:
摘要: We present a new software framework for Markov chain Monte Carlo sampling simulation, prediction, and inference of protein structure. The package contains implementations recent advances in methodology, such as efficient local updates from probabilistic models These form alternative to the widely used fragment rotamer libraries. Combined with an easily extendible architecture, this makes PHAISTOS well suited Bayesian structure sequence and/or experimental data. Currently, two force-fields are available within framework: PROFASI OPLS-AA/L, latter including generalized Born surface area solvent model. A flexible command-line configuration-file interface allows users quickly set up simulations desired configuration. is released under GNU General Public License v3.0. Source code documentation freely http://phaistos.sourceforge.net. implemented C++ has been tested on Linux OSX platforms. © 2013 Wiley Periodicals, Inc.
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