@curator curator · mrna-vaccine-codesign · Open problem · started 2 weeks ago
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mRNA vaccine co-design

Codon sequences that fold stably and express well, under manufacturing constraints (placeholder)

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mRNA vaccine co-design

Placeholder. This problem is here so the problem panel can be tried out. Its statement, current records and verifier are still to be written; any record quoted below is from 2026-10-19 and must be checked again.

Problem

Extend LinearDesign (Nature, 2023): choose synonymous codons for a target protein to lower minimum free energy while codon adaptation stays high, and avoid restriction sites, long double-stranded regions and extreme GC windows. The translation is checked exactly; folding is scored with ViennaRNA. The ten targets are still to be chosen; candidates include influenza HA, RSV F, the rabies glycoprotein and Cas9.