This respository contains code used to simulate evolution of cotranslational folding.
The main program, folding_evolution, is located at
src/app_folding_evolution/folding_evolution.cpp. It is code for an
MPI program. Supporting libraries are in src, although some are not
used. These libraries were written by others in the Shakhnovich
research group. I added a few functions to gencode. Some other
evolutionary simulation code written by others for other research
projects are in src.
To compile, an installation of HDF5 and MPI are needed. Furthermore,
the software suite latPack, https://github.com/proteins247/latPack,
must be installed. install_folding_evolution.sh is how I compile and
install my folding_evolution executable as a module on the Harvard
cluster; it should be modified before use elsewhere.
Several variants of the code are located in different branches:
new_fitness_eval: Same as master branch. Evolution of lattice protein sequences under a fitness function that evaluates cotranslational folding simulations.no_translation: Protein folding simulations for fitness evaluation are based on in vitro folding performance.stability_only: Fitness evaluation in which protein starts in folded state.translation_rate: Simulation mode where mutations are synonymous changes that only change the translation rate.
copyright 2020 by Victor Zhao
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.