The directories and scripts included were used to calculate evolutionary couplings between subunits of protein complexes and used the intermolecular coupling results to build integrative models.
################# EVCouplings ##########################
A basic configuration file is provided. This can be used in combination with the batchComplexCoupling.py script to compute pairwise evolutionary couplings between all proteins provided. For use:
python batchComplexCoupling.py -h
usage: batchComplexCoupling.py [-h] proteinlist [proteinlist ...]
Calculates pairwaise coevolutionary scores for protein pairs in an interaction group.
positional arguments: proteinlist list of uniprot ids of proteins in a complex groups.
optional arguments: -h, --help show this help message and exit
All protein scripts used are provided in their prospective directories.
The CoEv_analysis.ipynb notebook can be used for selection of appropriate intermolecular couplings for integrative modeling.
############## Integrative Modeling ####################
All input files and modeling scripts are provided in their prospective directories. Analysis scripts and exhaustive sampling scripts are provided as well.