PROFASI  Version 1.5
ProFASi: The Protein Folding and Aggregation Simulator

Introduction

PROFASI (PROtein Folding and Aggregation SImulator [I]) is a C++ program package for Monte Carlo simulations of proteins. It provides a set of tools for running simulations and analyzing the generated data. The model implemented uses an all-atom protein description, torsion angles as the degrees of freedom, and a simplified implicit solvent force field [II].

PROFASI is freely available under GNU General Public Licence (version 3). The current PROFASI version number is 1.5.

If you would like to get a copy of the PROFASI code, please go to the PROFASI request page.

If you have already used an older version of PROFASI, you can get an idea of the main recent changes by reading New in PROFASI version 1.5.

For a quick introduction to get started with PROFASI, take a look at Tutorial 1: A half an hour tour of PROFASI, which should give you a feel for it.

The Table of contents page will help you navigate through the documentation. If you have the doxygen program installed, you can generate this documentation locally by running "make docs" in the main PROFASI directory.

We welcome your involvement in this project. If you use PROFASI and find errors causing it to crash, hang, give wrong answers, etc., we would appreciate if you send a note to "profasi at thep.lu.se". Even better, if you fix the problem yourself, please send a patch file to the same email address. We will review and adjust the patch to ensure compatibility with other changes in the code, and then make it public, with due credit to you.

The following references provide an idea of the type of problems that have been studied using PROFASI: protein folding, misfolding and unfolding [III - VI], peptide aggregation [VII,VIII], and peptide folding in the presence of macromolecular crowders [IX,X]. The last two studies were done with an upcoming version of PROFASI (version 2), which we expect to make available later in 2016.

To cite PROFASI, please use [I] and, if appropriate, [II].


REFERENCES

[I] PROFASI: A Monte Carlo simulation package for protein folding and aggregation, A. Irbäck and S. Mohanty, J. Comput. Chem. 27, 1548−1555 (2006)
[II] An effective all-atom potential for proteins, A. Irbäck, S. Mitternacht and S. Mohanty, BMC Biophys. 2, 2 (2009)
[III] Simulation of Top7-CFr: A transient helix extension guides folding, S. Mohanty, J.H. Meinke, O. Zimmermann and U.H.E. Hansmann, Proc. Natl. Acad. Sci. USA 105, 8004−8007 (2008)
[IV] Changing the mechanical unfolding pathway of FnIII-10 by tuning the pulling strength, S. Mitternacht, S. Luccioli, A. Torcini, A. Imparato and A. Irbäck, Biophys. J. 96, 429−441 (2009)
[V] Folding of Top7 in unbiased all-atom Monte Carlo simulations, S. Mohanty, J.H. Meinke and O. Zimmermann, Proteins 81, 1446−1456 (2013)
[VI] Conformational and aggregation properties of the 1−93 fragment of apolipoprotein A-I, J. Petrlova, A. Bhattacherjee, W. Boomsma, S. Wallin, J.O. Lagerstedt and A. Irbäck, Protein Sci. 23, 1559−1571 (2014)
[VII] Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment, D.-W. Li, S. Mohanty, A. Irbäck and S. Huo, PLoS Comput. Biol. 4, e1000238 (2008)
[VIII] Monte Carlo study of the formation and conformational properties of dimers of Aβ42 variants, S. Mitternacht, I. Staneva, T. Härd and A. Irbäck, J. Mol. Biol. 410, 357−367 (2011)
[IX] Equilibrium simulation of trp-cage in the presence of protein crowders, A. Bille, B. Linse, S. Mohanty and A. Irbäck, J. Chem. Phys. 143, 175102 (2015)
[X] Peptide folding in the presence of interacting protein crowders, A. Bille, S. Mohanty and A. Irbäck, J. Chem. Phys. 144, 175105 (2016)

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2