A web service (PhosPPI) for Sequence-based Machine Learning Method for Predicting the Effects of Phosphorylation on Protein-Protein Interactions created by Xiaokun Hong, Jiyang Lv
Hong X, Lv J, Li Z, Xiong Y, Zhang J*, Chen HF*. Sequence-based machine learning method for predicting the effects of phosphorylation on protein-protein interactions. Int J Biol Macromol. 2023 Jul 15;243:125233. doi: 10.1016/j.ijbiomac.2023.125233. Epub 2023 Jun 6. PMID: 37290543.
<1>[email protected] <2>[email protected]
- Our Conda environment was created based on NetSurfP-3.0's Conda environment (Nucleic Acids Res,2022). *https://services.healthtech.dtu.dk/service.php?NetSurfP-3.0
- conda env create --file environment.yml
- conda activate nsp3
- python setup.py install
- pip3 install -r requirements.txt
*In addition, Web service and Machine Learning Python packages are required to install according to the following instructions:
- Install Web Service Python packages
- pip install
- Flask=1.1.2
- Flask-WTF=1.1.1
- WTForms=3.0.1
- Flask-Bootstrap=3.3.7.1
- Jinja2=2.11.3
- pandas=1.2.3
- gunicorn=19.9.0
- Other packages no need to install (latest version up to 2022-02-16; best to install them as network connection from China may fail)
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To perform PSI-BLAST to obtain PSSM features, ncbi-blast-2.9.0+-x64-linux are also needed to install. *https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/
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Install Machine Learning Python packages
- pip install sklearn=0.0
- pip install lightgbm=3.3.3