Evolutionary Constraints Guide AlphaFold2 Prediction of Alternative Conformations and Inform Rational Mutation Design

Code for clustering MSA representations to drive AF2 predictions toward alternative states.

Requirements:

localcolabfold (please follow the installation guidelines: localcolabfold-github)

As far as CUDA is concerned, we tested the code with the following configuration

$> nvidia-smi | grep CUDA 
| NVIDIA-SMI 530.30.02              Driver Version: 530.30.02    CUDA Version: 12.1     | 

Finally, we tested the code with the following python version

$> python3 --version
Python 3.10.2 

The dependencies are listed in the requirements.txt file, obtained with pip freeze in th environement we used to test our code. The general packages needed to run the code are listed in 'packages.txt'.

Installation:

- git clone https://github.com/RitAreaSciencePark/MSARC.git
- cd MSARC
- python -m venv conformer
- source conformer/bin/activate
- pip install -r packages.txt 

Input Format:

The input file "input_file_name" must be placed in the input_files folder and it should be a txt file containing the list of input ids and sequences in space separated format: "id sequence".
Example:

my_prot1 ABCDEFGH  
my_prot2 ILMNPQRS

Execution on a SLURM queue:

- sbatch launch.sh input_file_name