fusong-ju / ProFOLD

A protein 3D structure prediction application

ProFOLD

About The Project

The implementation of the paper "CopulaNet: Learning residue co-evolution directly from multiple sequence alignment for protein structure prediction".

Fusong Ju, Jianwei Zhu, Bin Shao, Lupeng Kong, Tie-Yan Liu, Wei-Mou Zheng and Dongbo Bu. CopulaNet: Learning residue co-evolution directly from multiple sequence alignment for protein structure prediction. Nature Communications. https://doi.org/10.1038/s41467-021-22869-8

Getting Started

Prerequisites

Install PyTorch 1.4+, PyRosetta, python 3.7+

Installation

1. Clone the repo

git clone https://github.com/fusong-ju/ProFOLD.git

2. Install python packages

cd ProFOLD
pip install -r requirements.txt

Usage

1. Generate aln format MSA for a given target sequence
2. Run ProFOLD

run_ProFOLD.sh <MSA> <output_dir>

Example

cd example
./run_example.sh

License

Distributed under the MIT License. See LICENSE for more information.