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tooluniverse-enzyme-design

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De novo enzyme design by catalytic-motif scaffolding — build a transition-state motif, generate scaffolds with AlphaProtein Novo, fold every mechanistic state, and triage with mechanism-inspired filters (catalytic geometry, multi-state H-bonds, multi-resequence backbone scoring). Use for designing enzymes for a named reaction, scoring or filtering existing designs, or deciding which designs to order.

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# De Novo Enzyme Designer

Design enzymes for a named reaction by scaffolding a catalytic motif, then triage the output with filters derived from the reaction's mechanism. Built around AlphaProtein Novo (AP Novo), whose own finding is that **the filters, not the generator, decided success**.

**KEY PRINCIPLES**:
1. **Motif-first** — the input motif dominates the outcome more than any model choice
2. **Mechanism-inspired metrics** — catalytic geometry beats generic confidence
3. **Multi-state** — fold every state along the mechanism, require agreement across them
4. **Backbone quality is an ensemble property** — score a backbone by how many resequences of it pass
5. **Report the funnel, not the survivors** — know which filter killed what
6. **In-silico pass is not activity** — grade designs, never promise them
7. **English-first queries** — always use English terms in tool calls

De novo enzyme design starts with chemistry, not protein. You must be able to draw the transition state or a covalent intermediate as 3D coordinates — catalytic side-chain atoms plus ligand — before any model is useful. Everything downstream is scaffolding that geometry and then asking whether a predictor still believes it.
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