PTM-CMGMS

Codes, datasets for "Improving PTM Site Prediction by Coupling of Multi-Granularity Structure and Multi-Scale Sequence Representation"

Datasets

Crotonylation：https://doi.org/10.1093/bioinformatics/btab712
Succinylation：https://www.nature.com/articles/s41598-022-21366-2
Nirosylation：https://link.springer.com/article/10.1186/s12859-023-05164-9#Sec2

Requirements

python==3.7.13
biopython==1.81
matplotlib==3.5.3
numpy==1.21.6
pandas==1.3.5
scikit_learn==1.0.2
torch==1.11.0+cu113
tqdm==4.65.0

Usage

We present an example based on the Crotonylation dataset and the result is saved under the folder result_of_Crotonylation/performance/

cd PTM-CMGMS/Codes

python Multi-granularity-Structure/main/main_MG.py  

python Multi-scale-Sequence/main_MS.py

Note:
Users can download the PDB structure file from https://alphafold.ebi.ac.uk/ or https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb and put them into folder Multi-granularity-Structure/pdb_structure to train prediction model (mkdssp：https://doi.org/10.1002/bip.360221211).

Contact

If you have any questions, please contact the email better_day_99@163.com.