About

What is RMDB?

The RNA Mapping Database (RMDB) is an archive of RNA structural mapping experiments — SHAPE, DMS, CMCT, 1M7, mutate-and-map, M2-seq, and related techniques. Each entry contains reactivity profiles for one or more RNA constructs under defined chemical and folding conditions, hand-curated and annotated by the depositors.

RMDB Website

This site is a static GitHub Pages mirror of the legacy RMDB Django site (rmdb.stanford.edu, 2012–2026). The dynamic site was retired in 2026 to make RMDB easier to maintain and contribute to: entries are now plain Markdown files in a public GitHub repository, RDAT files live alongside as version-controlled data, and updates happen via pull request.

What changed from the legacy site:

Detail pages still show the Construct and Citation panels, with the cached reactivity thumbnail. Interactive heatmap views, color-scale sliders, and the live annotation/reactivity sidebars are no longer rendered — the underlying data is still available via the .rdat download for use in rdat_kit or any RNA-mapping tool.
History tabs are gone; versioning is now via git history on the repo.
MyRMDB / Submit Entry / Analyze / Tools menus have been removed.
Deposit still documents the RDAT format and validation; Contribute explains the PR workflow for adding new entries.

Download all data

Every entry’s RDAT file lives as a GitHub Release asset, split across five subcategory releases so each stays well under GitHub’s 1,000-asset-per-release cap:

Release	Holds	Browse
`data-eterna`	Eterna and OpenKnot library experiments	181
`data-puzzle`	RNA Puzzles community blind-prediction challenges	94
`data-riboswitches`	Riboswitch families (TPP, SAM, glycine, FMN, ZTP, fluoride, …)	253
`data-rna-structures`	Ribosomal & transfer RNAs, viral RNAs (CoV-2, HIV, HCV, …), big mutate-and-map libraries	275
`data-general`	Everything else — heterogeneous tail	220

Browse and click

Open any of the release pages above and download individual .rdat files. Each asset is named <RMDB_ID>.rdat.

Grab one subcategory with the GitHub CLI

gh release download data-riboswitches \
    --repo DasLab/rmdb.github.io \
    --pattern "*.rdat" \
    --dir rdats/

Grab the entire database (all five releases)

for r in eterna puzzle riboswitches rna-structures general; do
    gh release download "data-$r" \
        --repo DasLab/rmdb.github.io \
        --pattern "*.rdat" \
        --dir rdats/
done

Streams directly from GitHub’s CDN — no bandwidth metering on either side, no need for a pre-built published_rdat.zip.

For per-entry programmatic access, each detail page’s “Download .rdat” button is a permanent direct link to that entry’s Release asset.

Citation

If you use RMDB data in your research, please cite:

Cordero P., Lucks J.B., Das R. An RNA Mapping DataBase for curating RNA structure mapping experiments. Bioinformatics 28(22): 3006–3008 (2012). doi:10.1093/bioinformatics/bts554

License

Database content (RDAT files, metadata, thumbnails): CC0 1.0 — public domain.
Site content (layout, prose, code): CC BY-SA 4.0.

Contact

Principal Investigator: Rhiju Das (Stanford Biochemistry, HHMI)
Site code: https://github.com/DasLab/rmdb.github.io
Issues / questions: please open a GitHub issue.