title: PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure.
abstract: 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.
authors.affiliation: Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark.
authors.forename: Wouter
authors.initials: W
authors.lastname: Boomsma
authors.forename: Jes
authors.initials: J
authors.lastname: Frellsen
authors.forename: Tim
authors.initials: T
authors.lastname: Harder
authors.forename: Sandro
authors.initials: S
authors.lastname: Bottaro
authors.forename: Kristoffer E
authors.initials: KE
authors.lastname: Johansson
authors.forename: Pengfei
authors.initials: P
authors.lastname: Tian
authors.forename: Kasper
authors.initials: K
authors.lastname: Stovgaard
authors.forename: Christian
authors.initials: C
authors.lastname: Andreetta
authors.forename: Simon
authors.initials: S
authors.lastname: Olsson
authors.forename: Jan B
authors.initials: JB
authors.lastname: Valentin
authors.forename: Lubomir D
authors.initials: LD
authors.lastname: Antonov
authors.forename: Anders S
authors.initials: AS
authors.lastname: Christensen
authors.forename: Mikael
authors.initials: M
authors.lastname: Borg
authors.forename: Jan H
authors.initials: JH
authors.lastname: Jensen
authors.forename: Kresten
authors.initials: K
authors.lastname: Lindorff-Larsen
authors.forename: Jesper
authors.initials: J
authors.lastname: Ferkinghoff-Borg
authors.forename: Thomas
authors.initials: T
authors.lastname: Hamelryck
mesh_terms: D001499:Bayes Theorem; D003198:Computer Simulation; D008390:Markov Chains; D008956:Models, Chemical; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins