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  3. Learning The Ptm Code Through A Coarse-to-fine Mechanism-aware Framework.
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  3. Learning The Ptm Code Through A Coarse-to-fine Mechanism-aware Framework.

Related Experiment Video

Decoding Natural Behavior from Neuroethological Embedding
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Published on: October 3, 2025

Learning the PTM code through a coarse-to-fine mechanism-aware framework.

Jingjie Zhang1, Hanqun Cao1, Zijun Gao1

  • 1Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China.

Nature Communications
|May 15, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

COMPASS-PTM deciphers the complex code of post-translational modifications (PTMs) by predicting sites and their regulatory enzymes. This framework enhances understanding of protein regulation and cellular signaling.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Proteomics

Background:

  • Post-translational modifications (PTMs) create a complex code regulating protein function and cellular signaling.
  • Predicting PTM sites and their associated enzymes is a significant challenge in biological research.

Purpose of the Study:

  • To introduce COMPASS-PTM, a novel framework for predicting PTM sites and assigning enzymes.
  • To unify residue-level PTM prediction with enzyme-substrate assignment.

Main Methods:

  • Developed a mechanism-aware, coarse-to-fine learning framework (COMPASS-PTM).
  • Integrated protein language models, physicochemical descriptors, and a crosstalk-aware prompting mechanism.
  • Addressed the long-tail distribution of PTM data.

Main Results:

  • Achieved a 122% relative improvement in F1-score for multi-label PTM site prediction.
  • Demonstrated a 54% gain in zero-shot enzyme assignment.
  • Recovered canonical kinase motifs and linked missense variants to PTM disruptions and network rewiring.

Conclusions:

  • COMPASS-PTM effectively unifies PTM site and enzyme prediction.
  • The framework learns the underlying grammar of protein regulation and signaling.
  • This approach advances the deciphering of the PTM code.