7. Protein Engineering Applications
This page of BioMoDes covers protein engineering applications — tools and studies demonstrating proteins redesigned or evolved for specific functions, including enzymes, therapeutics, biosensors, and more. Sections appear as papers are added.
7.1. Enzyme and Catalysis Engineering
2025 (Click to collapse/expand)
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CleaveNet: CleaveNet is an end-to-end AI pipeline that leverages deep learning for the design of protease substrates. The model generates peptide substrates and incorporates a conditioning tag to steer generation towards desired cleavage profiles. It can design efficient and selective substrates, revealing both well-established and previously uncharacterized cleavage motifs. Applied to matrix metalloproteinases, CleaveNet enhanced the scale, tunability, and efficiency of substrate design. The CleaveNet-generated substrates were experimentally validated through a large-scale in vitro screen, including designing highly selective substrates for MMP13.
Published: November 15, 2025
Paper
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