PHAISTOS a framework for Markov chain Monte Carlo simulation and inference of protein structure

PHAISTOS : a framework for Markov chain Monte Carlo simulation and inference of protein structure

Copyright © 2013 Wiley Periodicals, Inc.

Bibliographische Detailangaben
Veröffentlicht in:Journal of computational chemistry. - 1984. - 34(2013), 19 vom: 15. Juli, Seite 1697-705
1. Verfasser: Boomsma, Wouter (VerfasserIn)
Weitere Verfasser: Frellsen, Jes, Harder, Tim, Bottaro, Sandro, Johansson, Kristoffer E, Tian, Pengfei, Stovgaard, Kasper, Andreetta, Christian, Olsson, Simon, Valentin, Jan B, Antonov, Lubomir D, Christensen, Anders S, Borg, Mikael, Jensen, Jan H, Lindorff-Larsen, Kresten, Ferkinghoff-Borg, Jesper, Hamelryck, Thomas
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2013
Zugriff auf das übergeordnete Werk:Journal of computational chemistry
Schlagworte:Journal Article Research Support, Non-U.S. Gov't Proteins
Beschreibung
Zusammenfassung:Copyright © 2013 Wiley Periodicals, Inc.
We present a new software framework for Markov chain Monte Carlo sampling for simulation, prediction, and inference of protein structure. The software package contains implementations of recent advances in Monte Carlo methodology, such as efficient local updates and sampling from probabilistic models of local protein structure. These models form a probabilistic alternative to the widely used fragment and rotamer libraries. Combined with an easily extendible software architecture, this makes PHAISTOS well suited for Bayesian inference of protein structure from sequence and/or experimental data. Currently, two force-fields are available within the framework: PROFASI and OPLS-AA/L, the latter including the generalized Born surface area solvent model. A flexible command-line and configuration-file interface allows users quickly to set up simulations with the desired configuration. PHAISTOS is released under the GNU General Public License v3.0. Source code and documentation are freely available from http://phaistos.sourceforge.net. The software is implemented in C++ and has been tested on Linux and OSX platforms
Beschreibung:Date Completed 02.01.2014
Date Revised 14.06.2013
published: Print-Electronic
Citation Status MEDLINE
ISSN:1096-987X
DOI:10.1002/jcc.23292