A Python package to calculate, visualize and analyze correlation maps of proteins.
correlationplus contains four main scripts that you can use to calculate, visualize and analyze correlation maps of proteins. These correlations can be dynamical cross-correlations, linear mutual information, sequence based covariation/coevolution or any other pairwise coupling metric. You can use elastic network models or your molecular dynamics trajectories for calculation of dynamical correlations.
- Installation: https://www.youtube.com/watch?v=Fc_xpnrbbWU
- Calculate Module: https://www.youtube.com/watch?v=04b7mdulHW8
- Visualize Module: https://www.youtube.com/watch?v=HgUVAV1unXs
- Analyze Module: https://www.youtube.com/watch?v=04BwJDauOn4
- Sequence Conservation Analysis with CoeViz and correlationplus (Part 1): https://www.youtube.com/watch?v=ieu91glEd0s
- Sequence Conservation Analysis with CoeViz and correlationplus (Part 2): https://www.youtube.com/watch?v=BuxQNFoid1A
We recommend one of the installation methods for regular users:
The pip version required by some dependencies is >= 21.0.1, which is not the pip version bundle with python 3.(6,7,8) So, you have to update pip before installing correlationplus. Otherwise, you will have trouble during MDAnalysis dependency installation. For this reason, we strongly encourage you to install correlationplus in a virtualenv.
python3 -m venv correlationplus
cd correlationplus
source bin/activate
python3 -m pip install -U pip
python3 -m pip install correlationplusif you want to install it without using a virtualenv and encounter an error related to llvmlite, you can solve it as follows:
python3 -m pip install llvmlite --ignore-installed
python3 -m pip install correlationplusor if you do not have administration rights
python3 -m pip install --user llvmlite --ignore-installed
python3 -m pip install --user correlationplusconda install -c bioconda correlationplus
Most of the time, at least one these methods will be sufficient for the installation. However, if these two methods didn't work for any reason, you can take a look to 'Advanced Installation' instructions at https://correlationplus.readthedocs.io/en/latest/installation.html#advanced-installation.
There are four main scrips:
- calculate
- visualize
- analyze
- paths
You can find details of each script with the following commands:
correlationplus calculate -h
correlationplus visualize -h
correlationplus analyze -h
correlationplus paths -hGo to our readthedocs for detailed usage examples for each script.
If you use correlationplus, please cite us:
Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus Mustafa Tekpinar, Bertrand Neron, and Marc Delarue Journal of Chemical Information and Modeling Article ASAP DOI: 10.1021/acs.jcim.1c00742
correlationplus is developed and released under GNU Lesser GPL Licence. Please read to the COPYING and COPYING.LESSER files to know more.