The dbfold repository consists of a Python library for protein folding analysis and a Monte Carlo protein simulation program that uses a statistical potential.
Monte Carlo protein simulation. Capable of temperature replica exchange and restraints between residues (imitating disulfide bonds).
A Python library to analyze equilibrium and unfolding simulations to compute protein folding rates from detailed balance Authors: Amir Bitran, William M. Jacobs, Eugene Shakhnovich
Detailed instructions are provided in the IPython Notebook, dbfold_test.ipynb. If the MCPU package is used for simulation, a separate readme is provided within the MCPU directory.
In case one desires to update folding rates given new data, the notebook update_folding_rates_text.ipynb provides instructions for how to do this, but this should be done after initial calculation of folding rates (as explained in dbfold_test.ipynb).