GDFold2

GDFold2 is a protein folding environment. It is designed to rapidly and parallelly fold the protein structures based on arbitrary predicted constraints, which could be freely integrated into the environment as user-defined loss functions. We provide four folding modes to match the different geometric information. You can also customize the constraints according to your specific needs.

Getting Started

Install

git clone https://github.com/Gonglab-THU/GDFold2.git
cd GDFold2

GDFold2 Environment

conda env create -f environment.yml
conda activate GDFold2

Usage

1. GDFold2

• fold.py: input protein sequence (.fasta format) and predicted geometric information (.npz format) and output protein structure(s).

  python fold.py example/test.fasta example/test.npz example -d cuda
  

2. FastRelax

• Please install PyRosetta first!

• relax.py: perform FastRelax procedure.

  python relax.py --input example/101M_1.pdb --output example/relax.pdb
  

3. QAmodel

• QAmodel/run.py: input a directory containing multiple protein models folded by GDFold2 and output their ranking file rank.txt in the input directory.

  python QAmodel/run.py --input QAmodel/example
  

4. Dynamics

• Step 1: run Dynamics/pdb2cst.py to convert two conformational states of the same protein target into geometric constraint file (comb.npz).

  python Dynamics/pdb2cst.py --state1 Dynamics/1ake_A.pdb --state2 Dynamics/4ake_A.pdb --output Dynamics
  

• Step 2: run fold.py to predict the possible conformations in the transition path between the two conformational states.

  python fold.py Dynamics/comb.fasta Dynamics/comb.npz Dynamics/dynamics -n 50 -m Dynamics -d cuda
  

Web Server

We provide a web sever (GDFold2) for exploring protein structural dynamics. You can copy all the characters from Dynamics/1ake_A.pdb and Dynamics/4ake_A.pdb and paste them separately into the input box of the web server for testing.

Citation

If you use this code in your research, please cite our paper:

@article
author = {Mi, Tianyu and Gong, Haipeng},
title = {GDFold2: a fast and parallelizable protein folding environment with freely defined objective functions},
year = {2024},
doi = {10.1101/2024.03.13.584741}