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 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.

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Recommended citation: Chenao Li, Shuo Yan, Enyan Dai. (2025). "UniZyme: A Unified Protein Cleavage Site Predictor Enhanced with Enzyme Active-Site Knowledge." NeurIPS 2025.