PTraj-Diff

November 27, 2025 · View on GitHub

Implementation of[Efficient Generation of Protein and Protein-Protein Complex Dynamics via SE(3)-Parameterized Diffusion Models]

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News!

[2025/11/04] Available online Journal of Chemical Information and Modeling, 2025.

[2025/10/29] Accepted in Journal of Chemical Information and Modeling, 2025.

[2025/06/25] submission to Journal of Chemical Information and Modeling, 2025.

Installation

pip install torch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 --index-url https://download.pytorch.org/whl/cu121 
pip install pytorch_lightning==2.0.4 mdtraj==1.9.9 biopython==1.79
pip install wandb dm-tree einops torchdiffeq pyEMMA torchtyping transformers
pip install matplotlib==3.7.2 numpy==1.23.5  pandas==1.5.3

Model weights

The model weights used in the paper may be downloaded here:

https://drive.google.com/drive/folders/1vrmGUiZlDqikxunZY_C7HnjdfZk3ToSc?usp=sharing or https://zenodo.org/records/15687136

Inference

# protein
python  sim_inference_bert.py   --sim_ckpt  path/weights   --output_dir  path/to/save   --num_frames 3000  --split splits/chain_test_split.csv --num_rollouts 1 --xtc  --suffix _i10   --af3 --base_path_cif  sim_data/1phv

# protein-protein complex
python  sim_inference_bert.py   --sim_ckpt  path/weights   --output_dir  path/to/save   --num_frames 3000  --split splits/ppmid_test_x.csv --num_rollouts 1 --xtc --suffix _i10  --af3 --base_path_cif  sim_data/1brs

MD topology and coordinates

The topology and coordinates files are downloaded from:

 https://drive.google.com/drive/folders/1OrUq6BedZu9XyTolMmL0VkJrLYRCuQQn?usp=sharing or https://zenodo.org/records/15687037

Model Metrics

DockQ

DockQ: A Quality Measure for Protein-Protein Docking Models

https://github.com/bjornwallner/DockQ

  • Basu, S. and Wallner, B., 2016. DockQ: a quality measure for protein-protein docking models. PloS one, 11(8), p.e0161879.
  • Mirabello, C. and Wallner, B., 2024. DockQ v2: Improved automatic quality measure for protein multimers, nucleic acids, and small molecules. bioRxiv, pp.2024-05.
pip install DockQ
DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb

TM-Score

wget https://zhanggroup.org/TM-score/TMscore.cpp
g++ -static -O3 -ffast-math -lm -o TMscore TMscore.cpp
TMscore model.pdb native.pdb

Acknowledgement

The code is based on the following repositories:
https://github.com/bjing2016/mdgen.git

Lincense

Code is released under MIT LICENSE.

Citation

  • Kai Xu, Jianmin Wang, Mingquan Liu, Kewei Zhou, Shaolong Lin, Weihong Li, Lin Shi, Peng Zhou, Huanxiang Liu, and Xiaojun Yao. "EEfficient Generation of Protein and Protein–Protein Complex Dynamics via SE(3)-Parameterized Diffusion Models." Journal of Chemical Information and Modeling; doi: https://doi.org/10.1021/acs.jcim.5c01971
  • Jianmin Wang, Xun Wang, Yanyi Chu, Chunyan Li, Xue Li, Xiangyu Meng, Yitian Fang, Kyoung Tai No, Jiashun Mao, Xiangxiang Zeng. "Exploring the conformational ensembles of protein-protein complex with transformer-based generative model." Journal of Chemical Theory and Computation; doi: https://doi.org/10.1021/acs.jctc.4c00255