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Updated: Aug 6, 2026
09:10
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
GenPTM: A Generalizable Framework for Protein Post-Translational Modification Information Extraction from the
Shovan Bhowmik1, Karen Ross2, Chuming Chen1,3
1Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, United States.
Research Square
|July 17, 2026
Summary
GenPTM is a new tool that automatically identifies protein post-translational modifications (PTMs) and their sites from scientific literature. This PTM-agnostic approach advances automated knowledge discovery in proteomics.
Area of Science:
- Proteomics
- Bioinformatics
- Computational Biology
Background:
- Protein post-translational modifications (PTMs) are crucial for cellular functions.
- Existing PTM databases are limited in scope and update frequency.
- A gap exists between accumulating literature knowledge and curated PTM data.
Purpose of the Study:
- To develop a generalized information extraction (IE) tool for PTMs.
- To automate the identification of modified proteins and amino acid sites from literature.
- To address the limitations of PTM-specific extraction tools.
Main Methods:
- GenPTM utilizes a unified text representation strategy for PTMs.
- Generic placeholders replace PTM-specific terms to focus on modification patterns.
- A BiomedBERT-based classifier and post-processing module identify modified proteins and sites.
Main Results:
- GenPTM was trained on five major PTM types and evaluated on eight additional PTMs.
- Achieved high F1-scores (92%-96%) across various PTMs and evaluation categories.
- Demonstrated strong performance on less common PTMs like Citrullination and AMPylation.
Conclusions:
- GenPTM shows strong generalization capabilities for PTM-agnostic IE.
- Provides a viable solution for automated PTM knowledge discovery.
- Facilitates comprehensive understanding of PTMs in proteomics research.
Keywords:
BERTBioNLPInformation ExtractionPhosphorylationPost-Translational ModificationRelation ExtractionText-MiningMore Related Videos
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These groups modify specific amino acids in a protein.
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These groups modify specific amino acids in a protein.
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