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.
- RNAStructure - Contains useful utilities, including
ct2dot, which allow the conversion between the CT file format and the Dot Bracket file format.
- EternaBrain - Source code for
- CDPfold - Solve the inverse RNA folding problem using reinforcement learning.
- jadeshi/SentRNA - Solve the inverse RNA folding problem using reinforcement learning.