Graph-Based Protein Design

This repo contains code for Generative Models for Graph-Based Protein Design by John Ingraham, Vikas Garg, Regina Barzilay and Tommi Jaakkola, NeurIPS 2019.

Our approach 'designs' protein sequences for target 3D structures via a graph-conditioned, autoregressive language model:

Overview

• struct2seq/ contains model code
• experiments/ contains scripts for training and evaluating the model
• data/ contains scripts for building and processing datasets in the paper

Requirements

• Python >= 3.0
• PyTorch >= 1.0
• Numpy

Citation

@inproceedings{ingraham2019generative,
author = {Ingraham, John and Garg, Vikas K and Barzilay, Regina and Jaakkola, Tommi},
title = {Generative Models for Graph-Based Protein Design},
booktitle = {Advances in Neural Information Processing Systems}
year = {2019}
}