ORIGAMI

Orientation-Aware Graph Neural Network for Assessing Multimeric Interfaces of Protein Complex Structures

Installation

The project requires several ML-specific libraries, it's easier to setup with Anaconda:

1. Clone the repository

   git clone https://github.com/Bhattacharya-Lab/ORIGAMI.git
   cd ORIGAMI

2. Set up the environment

   conda env create -f origami_environment.yml
   conda activate origami

3. Install

   pip install -e .

Usage

We provide a command-line interface for ORIGAMI that can easily be used to score protein-protein complexes. The command-line interface can be used as follows:

$ origami-score -h
usage: origami-score [-h] [--checkpoint CHECKPOINT] [--config CONFIG] [--device DEVICE] [--output OUTPUT] [--json] pdb

Score a protein-protein complex using ORIGAMI.

positional arguments:
  pdb                   Path to the input PDB file containing two chains.

optional arguments:
  -h, --help            show this help message and exit
  --checkpoint CHECKPOINT
                        Path to the pretrained checkpoint (.pt).
  --config CONFIG       YAML configuration used during training.
  --device DEVICE       Torch device identifier (e.g. cuda, cuda:0, cpu).
  --output OUTPUT       Optional path to write the prediction score as JSON.
  --json                Print the prediction as JSON instead of a plain float.

Example, score the H1245TS028_4.pdb complex (in ORIGAMI/example)

$ conda activate origami
(origami) $ origami-score ORIGAMI/example/H1245TS028_4.pdb
(origami) $ origami-score /home/grads/xinyu0110/ORIGAMI/example/H1245TS028_4.pdb
Predicted iLDDT for protein complex H1245TS028_4.pdb is: 0.752040

From the output above you can see that the predicted iLDDT for the H1245TS028_4 complex is 0.752040

Contact

For questions or collaboration requests, reach out to the maintainers:

• Xinyu Wang — Virginia Tech — xinyu0110@vt.edu