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

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 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 inthis https URL.

@article{li2025_2502.06914,
  title={ UniZyme: A Unified Protein Cleavage Site Predictor Enhanced with Enzyme Active-Site Knowledge },
  author={ Chenao Li and Shuo Yan and Enyan Dai },
  journal={arXiv preprint arXiv:2502.06914},
  year={ 2025 }
}