correlationplus

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.

The easiest way to test correlationplus is to use it via Google Colab. Click correlationplus.ipynb to use correlationplus without installing it on your computer.

Video Tutorials

• 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

Installation

We recommend one of the installation methods for regular users:

with pip

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 correlationplus

if 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 correlationplus

or if you do not have administration rights

python3 -m pip install --user llvmlite --ignore-installed
python3 -m pip install --user correlationplus

with conda

conda 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.

Quickstart

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 -h

Go to our readthedocs for detailed usage examples for each script.

Cite

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 DOI: 10.1021/acs.jcim.1c00742

Licensing

correlationplus is developed and released under GNU Lesser GPL Licence. Please read to the COPYING and COPYING.LESSER files to know more.