What is this repository for?

• This repository is for holding the Command Line Interface in python for the SCA toolbox (http://systems.swmed.edu/rr_lab/sca.html) We have recreated the toolbox in python for further use in a Pymol plugin for visualization
• Beta - test version
• Learn Markdown

What is SCA?

• SCA is a computation technique to determine potential allosteric sites in protein families

• based on evolutionary coupling between amino acid sequences in proteins.

• Note that there is a lower bound on number of sequences used in an MSA determined by binomial

• distribution of frequencies of amino acids and KL entropy function. Around 100 is what the

• notes on SCA calculations suggest.

How do I get set up?

• Summary of set up
• Configuration
• Dependencies: Procedure for Linux machines:

  1. SciPy has the following dependencies which need to be installed globally.

  2. Requirements.txt contains the list of the libraries/packages required.

The following commands can be used to install all the dependencies:

#!
sudo apt-get install gfortran libopenblas-dev liblapack-dev
pip install -r <location of requirements.txt file>

• Database configuration
• How to run tests
• Deployment instructions

Contribution guidelines

• Writing tests
• Code review
• Other guidelines

Who do I talk to?

• Contact - robin{.}philip{.}[email protected]
• Remove the {.} before sending