New Tools
October 5, 2026RfamRNA family records, consensus structures, and genome-wide hit coordinates from the Rfam database.
September 30, 2026MinervaAlignment-free maps of RNA base pairing, protein contacts, and repeats across microbial genomes.
September 30, 2026gLM2Masked language model reading protein-coding and intergenic DNA together as one genomic context.
September 2, 2026Genomic IntelligenceSeven DNA language models scoring promoters, splice sites, enhancers, chromatin, and expression.
August 5, 2026Primer3Melting temperature, hairpin and dimer stability, and GC content for a DNA oligo.
August 5, 2026CodonFMCodon-level masked language model for coding-sequence fitness, embeddings, and design.
August 4, 2026AutoDock VinaSmall-molecule docking into a rigid receptor, returning ranked poses with affinity scores.
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.Commit Timeline
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.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.