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Anders Irbäck. Photo.

Anders Irbäck

Professor

Anders Irbäck. Photo.

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

Author

  • Anders Irbäck
  • Sandipan Mohanty

Summary, in English

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.

Department/s

  • Computational Biology and Biological Physics
  • Department of Astronomy and Theoretical Physics

Publishing year

2006

Language

English

Pages

1548-1555

Publication/Series

Journal of Computational Chemistry

Volume

27

Issue

13

Document type

Journal article

Publisher

John Wiley and Sons

Topic

  • Biophysics

Keywords

  • protein folding
  • Monte Carlo
  • all-atom model
  • plus
  • protein aggregation
  • C

Status

Published

ISBN/ISSN/Other

  • ISSN: 1096-987X