j3xugit/glinter

Graph Learning of INTER-protein contacts

GLINTER: Graph Learning of INTER-protein contacts

Installation

Require python>=3.7

Clone the repository and install it

git clone https://github.com/zw2x/glinter.git
cd glinter
pip install -e .

Manually install the following softwares and models

• torch>=1.6
• torch_geometric
• MSMS
• reduce
• hh-suite
• esm_msa1_t12_100M_UR50S

The taxonomy database and model weights can be found at

Usage

The following commands are executed in the repository glinter.

Replace the environment variables in set_env.sh and run.sh in the scripts directory by your installation paths and then run

source scripts/set_env.sh

There are two example pdb files in the examples directory. To predict the inter-protein contacts between 1a59A.pdb and 1a59B.pdb, run

scripts/run.sh examples/1a59A.pdb examples/1a59B.pdb examples/

The output is examples/1a59A:1a59B/1a59A:1a59B.out.pkl