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PROFASI: A Monte Carlo simulation package for protein folding and aggregation

Irbäck, Anders LU orcid and Mohanty, Sandipan LU (2006) In Journal of Computational Chemistry 27(13). p.1548-1555
Abstract
We present a flexible and efficient program package written in C++, PROFASI, for simulating protein folding and aggregation. The systems are modeled using an all-atom description of the protein chains with only torsional degrees of freedom, and implicit water. The program package has a modular structure that makes the interaction potential easy to modify. The currently implemented potential is able to fold several peptides with about 20 residues, and has also been used to study aggregation and force-induced unfolding. The simulation methods implemented in PROFASI are Monte Carlo-based and include a semilocal move and simulated tempering. Adding new updates is easy. The code runs fast in both single- and multi-chain applications, as is... (More)
We present a flexible and efficient program package written in C++, PROFASI, for simulating protein folding and aggregation. The systems are modeled using an all-atom description of the protein chains with only torsional degrees of freedom, and implicit water. The program package has a modular structure that makes the interaction potential easy to modify. The currently implemented potential is able to fold several peptides with about 20 residues, and has also been used to study aggregation and force-induced unfolding. The simulation methods implemented in PROFASI are Monte Carlo-based and include a semilocal move and simulated tempering. Adding new updates is easy. The code runs fast in both single- and multi-chain applications, as is illustrated by several examples. (C) 2006 Wiley Periodicals, Inc. (Less)
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author
and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
protein folding, Monte Carlo, all-atom model, plus, protein aggregation, C
in
Journal of Computational Chemistry
volume
27
issue
13
pages
1548 - 1555
publisher
John Wiley & Sons Inc.
external identifiers
  • wos:000240267200008
  • scopus:33748604047
ISSN
1096-987X
DOI
10.1002/jcc.20452
language
English
LU publication?
yes
id
9f7e5d42-efef-4908-a9c9-8c22c65a5fac (old id 394721)
date added to LUP
2016-04-01 15:42:06
date last changed
2024-04-11 11:43:38
@article{9f7e5d42-efef-4908-a9c9-8c22c65a5fac,
  abstract     = {{We present a flexible and efficient program package written in C++, PROFASI, for simulating protein folding and aggregation. The systems are modeled using an all-atom description of the protein chains with only torsional degrees of freedom, and implicit water. The program package has a modular structure that makes the interaction potential easy to modify. The currently implemented potential is able to fold several peptides with about 20 residues, and has also been used to study aggregation and force-induced unfolding. The simulation methods implemented in PROFASI are Monte Carlo-based and include a semilocal move and simulated tempering. Adding new updates is easy. The code runs fast in both single- and multi-chain applications, as is illustrated by several examples. (C) 2006 Wiley Periodicals, Inc.}},
  author       = {{Irbäck, Anders and Mohanty, Sandipan}},
  issn         = {{1096-987X}},
  keywords     = {{protein folding; Monte Carlo; all-atom model; plus; protein aggregation; C}},
  language     = {{eng}},
  number       = {{13}},
  pages        = {{1548--1555}},
  publisher    = {{John Wiley & Sons Inc.}},
  series       = {{Journal of Computational Chemistry}},
  title        = {{PROFASI: A Monte Carlo simulation package for protein folding and aggregation}},
  url          = {{http://dx.doi.org/10.1002/jcc.20452}},
  doi          = {{10.1002/jcc.20452}},
  volume       = {{27}},
  year         = {{2006}},
}