> ## Documentation Index > Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt > Use this file to discover all available pages before exploring further. # Change Log > New tools and recent development across the Proto language and tools layers 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.
## New Tools
July 24, 2026 OpenDDE All-atom co-folding for complexes of proteins, DNA, RNA, ligands, and ions. July 23, 2026 PARADE Cell-type-specific UTR activity and 3' UTR mRNA stability prediction. June 25, 2026 Metal3D Zinc-binding site prediction and coordinates from a protein structure.
## Commit Timeline
Modal Modal The tools layer gained a deployment layer for the whole catalog. 54 applications serve 99 tools on [Modal](https://modal.com).
OpenDDE was added to the structure prediction category.
## 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. Fork proto-tools and open a pull request. CONTRIBUTING.md documents the layout and conventions. Describe what you would like to see in Proto and how we can assist.