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 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
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
], peptide aggregation [VII
], and peptide folding in the presence of macromolecular crowders [IX
]. 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