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PROFASI: A Monte Carlo simulation package for protein folding and aggregation
Author(s) -
Irbäck Anders,
Mohanty Sandipan
Publication year - 2006
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20452
Subject(s) - parallel tempering , computer science , monte carlo method , modular design , computational science , folding (dsp implementation) , molecular dynamics , degrees of freedom (physics and chemistry) , monte carlo molecular modeling , chemistry , markov chain monte carlo , computational chemistry , programming language , mechanical engineering , physics , mathematics , engineering , thermodynamics , statistics
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. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1548–1555, 2006