Datasets:

RosettaCommons
/

PTMint

pretty_name: >-
  PTMint database of experimentally verified PTM regulation on protein–protein
  interaction
repo: 10.5281/zenodo.15164650
homepage: https://ptmint.sjtu.edu.cn/
license: mit
tags:
  - post-translational-modifications
  - phosphorylation
  - acetylation
  - methylation
  - sumoylation
  - ubiquitylation
  - glycosylation
  - protein-protein-interaction
  - structural-biology
  - bioinformatics
configs:
  - config_name: main
    data_files:
      - split: ptmint_general
        path: data/ptmint_all_with_splits.csv
      - split: ptmint_phospho_interfaces
        path: data/ptmint_interface_phospho_with_splits.csv

PTMint

This dataset is derived from PTMint (https://ptmint.sjtu.edu.cn/), (Post Translational Modifications that are associated with Protein-Protein Interactions) that contains manually curated complete experimental evidence of the PTM effecting on protein-protein interactions in multiple organisms, including H. sapines, A. thaliana, C. elegans, D. melanogaster, S. cerevisiae and S. pombe. This Hugging Face dataset repository provides PTMint-derived tables including a precomputed split column for cluster-aware precomputed splits. Clusters were determined by consensus site identity.

Dataset Summary

Domain: protein biology / interactomics / PTM regulation
Description: PTM event mapped to a PPI and its effect on said PPI (Enhance: Increase affinity and Inhibit: Decrease affinity).
Primary uses:
- Benchmarking models that predict PTM-dependent PPI regulation (enhance/inhibit)
- PTM sites mapped to structural interfaces

Citation

When referring to PTMint, please cite:

Hong X, Li N, Lv J, Zhang Y, Li J, Zhang J, Chen HF. PTMint database of experimentally verified PTM regulation on protein-protein interaction. Bioinformatics. 2023;39(1):btac823. doi:10.1093/bioinformatics/btac823. PMID: 36548389.

Data Files

This repository contains two datasets:

ptmint_general
- Path: data/ptmint_all_with_splits.csv
- Contents: PTMint-derived records (all PTM types included and sites both in the PPI interface and outside the interface).
ptmint_phospho_interfaces
- Path: data/ptmint_interface_phospho_with_splits.csv
- Contents: a phosphorylation-focused subset restricted to records where the PTM site is mapped to a protein–protein interface (as defined by your preprocessing pipeline in src).

Dataset Statistics

The current version includes 2477 Non-redundant PTM sites and 2371 Protein–protein pairs.

Table 1. Summary of PTM effects on protein–protein interactions

PTM types	PTM sites	Enhance	Inhibit	Interface (%)
Acetylation	K	192	125	17%
Glycosylation	S, T	5	0	0%
Methylation	K, R	145	22	24%
Phosphorylation	S, T, Y	2925	1580	16%
Sumoylation	K	57	26	8%
Ubiquitylation	K	67	12	31%

Main Experimental Methods

Method

Capture information from their website by analyzing the HTML for each entry to salvage the structures + the origin and additional annotations to the structure. Several of these webpages were down. Hence, on top of HTML analysis, extracted the sequences from UNIPROT for all proteins and aligned sequences with the ones from the complexes to identify corresponding structures.

License

This dataset repository: MIT License for educational purposes only.
Underlying PTMint database/publication: please cite the PTMint paper when using these data.

Citation

If you use this dataset in your research, please cite the original PTMint publication:

Hong X, Li N, Lv J, Zhang Y, Li J, Zhang J, Chen HF.
PTMint database of experimentally verified PTM regulation on protein–protein interaction.
Bioinformatics. 2023;39(1):btac823.
https://doi.org/10.1093/bioinformatics/btac823

BibTeX:

@article{hong2023ptmint,
  title   = {PTMint database of experimentally verified PTM regulation on protein–protein interaction},
  author  = {Hong, Xue and Li, Ning and Lv, Jia and Zhang, Yu and Li, Jie and Zhang, Jie and Chen, H. F.},
  journal = {Bioinformatics},
  volume  = {39},
  number  = {1},
  pages   = {btac823},
  year    = {2023},
  doi     = {10.1093/bioinformatics/btac823},
  pmid    = {36548389}
}

Contact

For Huggingface database: Lina Maria Pena Pardo / linamp (at) umich.edu