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Proto is organized in two layers. The language contains the optimization engine together with its constraints, generators, and optimizers. The tools layer contains the bioinformatics models that the language invokes. The chart below records weekly commit activity in both layers. Hovering a week shows the commit counts for that week, along with any commit from it that carries a write-up in the timeline below.

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New Tools

July 24, 2026OpenDDEAll-atom co-folding for complexes of proteins, DNA, RNA, ligands, and ions.July 23, 2026PARADECell-type-specific UTR activity and 3’ UTR mRNA stability prediction.June 25, 2026Metal3DZinc-binding site prediction and coordinates from a protein structure.

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Commit Timeline

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Tools layer
The tools layer gained a deployment layer for the whole catalog. 54 applications serve 99 tools on Modal.
OpenDDE was added to the structure prediction category.

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Contribute

The tool catalog is extended through contributions. To add a tool, fork the repository and open a pull request; we will assist with the integration.

Add a tool

Fork proto-tools and open a pull request. CONTRIBUTING.md documents the layout and conventions.

Contact us

Describe what you would like to see in Proto and how we can assist.