OpenKnot RNA Pseudoknots – RFDpoly 3D Structures

This dataset contains computationally generated RNA 3D structures resembling pseudoknot topologies that were targets of the Eterna OpenKnot competiton [1]. These structures were produced by RFDpoly [2], through base pair template-conditioned structure generation.

Each zip file contains strutures corresponding to different OpenKnot competition Rounds, and different filtering methods, described below:

round_7a__top_backbones.zipTop RNA backbones generated for OpenKnot Round 7a puzzles, ranked, filtered, and selected based on F1-score similarity between the secondary structure of a given pseudoknot puzzle and the secondary structure of the provided 3D structure.

round_7a_filtered_RFdiff_backbone_dataset.tar.gzFull set of RNA backbones generated for OpenKnot Round 7a filtered filtered by F1-score similarity between the secondary structure of a given pseudoknot puzzle and the secondary structure of the provided 3D structure.

round_7b__by_design2target.zipTop RNA backbones generated for OpenKnot Round 7b puzzles, ranked, filtered, and selected based on F1-score similarity between the secondary structure of a given pseudoknot puzzle and the secondary structure of the provided 3D structure.

round_7b__by_pred2target.zipTop RNA backbones generated for OpenKnot Round 7b puzzles, ranked, filtered, and selected based on F1-score similarity between the secondary structure of a given pseudoknot puzzle and the secondary structure of AlphaFold3-predictions [3] from NA-MPNN sequences [4] that were designed using the provided 3D structure as inputs for inverse-folding.

RFdiff_pseudocycle_pdbs.zipBonus dataset. 3D structures for custom de novo RNA pseudocycles produced by RFDpoly. These were not official targets of previous OpenKnot rounds, but were characterized via SHAPE-seq in a similar manner.

References:

[1]  Additional information about the Eterna OpenKnot challenge (including puzzles and secondary structures) is available at: https://eternagame.org/challenges/11843006

[2]  Favor, Andrew, Riley Quijano, Elizaveta Chernova, Andrew Kubaney, Connor Weidle, Morgan A. Esler, Lilian McHugh et al. "De novo design of RNA and nucleoprotein complexes." bioRxiv (2025): 2025-10.

[3] Abramson, Josh, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ronneberger et al. "Accurate structure prediction of biomolecular interactions with AlphaFold 3." Nature 630, no. 8016 (2024): 493-500.

[4]  Kubaney, Andrew, Andrew Favor, Lilian McHugh, Raktim Mitra, Robert Pecoraro, Justas Dauparas, Cameron Glasscock, and David Baker. "RNA sequence design and protein–DNA specificity prediction with NA-MPNN." bioRxiv (2025): 2025-10.