mlsanityData to 14 Oct 2026

UniZyme: A Unified Protein Cleavage Site Predictor Enhanced with Enzyme Active-Site Knowledge

arXiv 2502.06914 ↗First posted 10 Feb 2025q-bio.QM cs.AI cs.LGcited by 3

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Abstract (arXiv)

Enzyme-catalyzed protein cleavage is essential for many biological functions. Accurate prediction of cleavage sites can facilitate various applications such as drug development, enzyme design, and a deeper understanding of biological mechanisms. However, most existing models are restricted to an individual enzyme, which neglects shared knowledge of enzymes and fails to generalize to novel enzymes. Thus, we introduce a unified protein cleavage site predictor named UniZyme, which can generalize across diverse enzymes. To enhance the enzyme encoding for the protein cleavage site prediction, UniZyme employs a novel biochemically-informed model architecture along with active-site knowledge of proteolytic enzymes. Extensive experiments demonstrate that UniZyme achieves high accuracy in predicting cleavage sites across a range of proteolytic enzymes, including unseen enzymes. The code is available in https://github.com/Ao-LiChen/UniZyme

Key facts. Cited by 3 papers in the map (data through 14 Oct 2026). Builds on 11 of its 64 references that are in the map. First posted on arXiv 10 Feb 2025.

Builds on

11 of 64 references.

References · 11

  1. 2021E(n) Equivariant Graph Neural Networkscited by 965
  2. 2020Learning from Protein Structure with Geometric Vector Perceptronscited by 313
  3. 2022Protein Representation Learning by Geometric Structure Pretrainingcited by 162
  4. 2022A Comprehensive Survey on Trustworthy Graph Neural Networks: Privacy, Robustness, Fairness, and Explainabilitycited by 118
  5. 2022One Transformer Can Understand Both 2D & 3D Molecular Datacited by 77
  6. 2021Towards Self-Explainable Graph Neural Networkcited by 75
  7. 2022Towards Prototype-Based Self-Explainable Graph Neural Networkcited by 14
  8. 2023A Unified Framework of Graph Information Bottleneck for Robustness and Membership Privacycited by 14
  9. 2024ReactZyme: A Benchmark for Enzyme-Reaction Predictioncited by 13
  10. 2024Beyond Sequence: Impact of Geometric Context for RNA Property Predictioncited by 8
  11. 2021Labeled Data Generation with Inexact Supervisioncited by 2

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Cited by year (2026 to 14 Oct)

Citing papers per year: 2025: 1; 2026: 2.

3 papers.

  1. 2025DualEquiNet: A Dual-Space Hierarchical Equivariant Network for Large Biomoleculescited by 5
  2. 2026Route to Rome Attack: Directing LLM Routers to Expensive Models via Adversarial Suffix Optimizationcited by 5
  3. 2026From Snapshots to Symphonies: The Evolution of Protein Prediction from Static Structures to Generative Dynamics and Multimodal Interactionscited by 0