mRNA Secondary Structure Catalog

Browsable, forna-style catalogs of DeRNA+Knotty mRNA secondary structures (DeRNA-generated sequences, folded with Knotty).

🔎 Live site: https://aspuru-guzik-group.github.io/mrna-structure-catalog/

Catalog	Contents
AA=20 (1000)	all 1000 AA=20 structures — 149 PK / 851 non-PK
AA=60 (99)	99 AA=60 structures — 6 PK / 93 non-PK
All pseudoknotted	all 823 pseudoknotted structures, AA 4–60

Each card shows the structure, a PK / Non-PK badge, AA-length · nt · bp · PK-bp · MFE, and the protein (AA) sequence (toggle-able). Sort by AA length, index, base pairs, MFE, or PK pairs.

Rendering

• Non-pseudoknotted structures use forna's force-directed layout (compact, readable), rendered headlessly into static SVG.
• Pseudoknotted structures use ViennaRNA NAView, with crossing (pseudoknot) base pairs drawn as red links (force layouts tangle pseudoknots).

Pages are served as static HTML; each catalog references a sibling _assets/ folder of per-structure SVGs (lazy-loaded via <img>).

Regenerate

Code under generator/. Requires ViennaRNA (NAView) and, for the forna-force path, Node + a system Chrome (forna's JS/CSS are vendored under generator/prerender/forna_vendor/, so generation is offline). Input is the per-sample parquet from the DeRNA+Knotty profiling run (issue #47).

cd generator && (cd prerender && npm install)   # once
PQ=path/to/pk_profile.parquet
python3 structure_catalog.py --parquet $PQ --aa-len 20 \
  --prerender-hybrid --forna-jobs 6 --prerender img --out ../docs/aa20_1000.html

Data: mRNA-project/mrna-transformer-data (issue #47 profiling run). Model and analysis code live in the (private) aspuru-guzik-group/mrna-transformer repository.