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Inverse folding problem

The goal of the inverse RNA folding problem is to generate RNA sequences which fold into a pre-determined shape.

Note: The inverse RNA folding problem may be more of a sampling problem than a constraint satisfaction problem, since the number of constraints per ribonucleotide is much smaller but the number of off-target foldings is much higher.


  • RNA STRAND v2.0 - Contains ~5000 RNA sequences and base-pairings. Has not been updated in ~10 years.
  • bpRNA-1m - Contains ~100,000 RNA sequences and base-pairings. Published in 2018.
  • Eterna100 - A representative dataset of RNA structures solved by Eterna players.
  • RNAiFold 2.0 - 63 experimentally-synthesized targets.
  • CASP RNA Challenge — CASP is planning to include RNA puzzles in the future.