qProtein: Exploring Physical Features of Protein Thermostability Based on Structural Proteomics

Key features

✨ Ingrated platform: An automated workflow integrating a variety of bioinformatics tools and a deep learning model.

✨ Batch Processing: Transform multiple protein sequences to structures.

✨ Interaction Analysis: Compute four major types of physical interactions: hydrogen bonds, electrostatic interactions, hydrophobic clusters, and disulfide bonds.

✨ Overall and Local Structural Analysis: Analyze local structural features within targeted regions.

Install qProtein

git clone https://github.com/bj600800/qProtein.git

cd qProtein

conda create -n qprotein python=3.9
conda activate qprotein

pip install biotite==0.37.0 
pip install pdb2pqr
pip install tqdm
pip install numpy==1.23.5
pip install biopython==1.83

Additional requirements

Notice: Modify config params in run_qprotein.py for your installation.

Structural alignment for local structure analysis

For Win USalign.exe

For Linux USalign

Configure ESMFold for prediction module

ESMFold

Run qProtein

Getting structures

python run_qprotein.py --id test/id.txt --work_dir test

Using user-prepared structures for overall analysis

python run_qprotein.py --work_dir test --pre_pdb test\pdb

Local analysis

Notice: Four params --template_name, --template_active_res --dist1, and --dist2 should be defined by users depending on the task requirement.

For further details, please refer to the paper.

python run_qprotein.py --id test/id.txt --work_dir test --local --template_name P33557 --template_active_res 33,35,37,64,66,91,93,97,99,106,108,115,116,118,142,146,147,148,154,156,158,191,197,199,200 --dist1 12 --dist2 15

Using ESMFold model for predicting protein structures

python run_qprotein.py --fasta test/sequence.fasta --work_dir test --local --template_name P33557_seq --template_active_res 33,35,37,64,66,91,93,97,99,106,108,115,116,118,142,146,147,148,154,156,158,191,197,199,200 --dist1 12 --dist2 15

Citation

@article{dou2024qprotein,
  title={qProtein: Exploring Physical Features of Protein Thermostability Based on Structural Proteomics},
  author={Dou, Zhixin and He, Jiaxin and Han, Chao and Wu, Xiuyun and Wan, Lin and Yang, Jian and Zheng, Yanwei and Gong, Bin and Wang, Lushan},
  journal={Journal of Chemical Information and Modeling},
  volume={64},
  number={20},
  pages={7885--7894},
  year={2024},
  publisher={ACS Publications}
  doi={10.1021/acs.jcim.4c01303}
}

Online web-server (for ID mode only with seq2struct)

http://qprotein.sdu.edu.cn:8888

Schematic diagram of interaction algorithm