Our paper with @eternagame, 5 AI teams, and cryo-EM collabs on de novo design of #RNA pseudoknots with #deeplearning is out in @science.org! Comes with a provocative commentary on RNA structure prediction by @amustoe.bsky.social lab! doi.org/10.1126/scie... doi.org/10.1126/scie...

Jill Townley@jilltownley.bsky.social · last mo.

How do researchers design an RNA in 3D when no accurate 3D prediction model exists? Eterna's collaboration with the @rdaslab.bsky.social at Stanford was able to design novel pseudoknots using a blend of secondary structure prediction and GenAI design methods. 🧪 #RNAsky

Finally, 3D #cryoEM structure of a nucleotide polymerizing #RNA that copies #RNA to #RNA: tC19z, evolved at @mrclmb.ac.uk 15 y ago! www.biorxiv.org/content/10.6... @szokoli.bsky.social Jason Hingey, Dan Haack, Vivian Wu Nick Spellmon @navtejtoor.bsky.social @hhmijanelia.bsky.social

We and @eternagame.org are joining the quest to find a molecule that can sustainably replicate itself. Pilot results on first 1000 designs are posted, next up will be million-design-scale expts. Come design at eternagame.org/labs/14660266 by Aug 31, 2026! #RNAworld

Eterna@eternagame.org · 2mo ago

Our Replicase pilot results found that the catalytic activity and copyability of the 71-89 polymerase ribozyme can be improved! We have launched a new puzzle for finding a version that excels at both properties simultaneously. Comp methods are encouraged to submit designs!

RNA flexible? Maybe we can model that. First blind test of RNA 3D *ensemble* prediction — ligand-free SAMURI ribozyme (displayed on a group II intron scaffold) -- #MD and #deeplearning methods welcome, deadline Aug 22, 2026: predictioncenter.org/casp17/targe...

OpenKnot Round 9 features secondary structures designed by players to create compact, pseudoknotted RNA using 240 bases. GenAI teams also will be testing whether their methods can perform as well as the expert players at a longer length. Check out the puzzle at: eternagame.org/labs/14343053

Pseudoknots, AI, and preview of Eterna's first RNA replicase results at EternaCon 12, virtual on Sunday July 26, 2026! Preregister for free at: eternagame.org/eternacon/2026

Can humans+AI get 1M #cryoEM-able #RNA structures? Phase 1: humans design 1000 pseudoknot structures @eternagame.org by Jul 19. Phase 2: AIs design 1000 sequences for each by Jul 31. Come join! Latest phase of the OpenKnot challenge eternagame.org/challenges/1... #citsci #RNAsky

Eterna@eternagame.org · 3mo ago

Eterna's newest puzzle challenges players to design 240-base RNA strands that will fold into compact pseudoknots. The puzzle provides a metric for counting the number of pairs that cross to form large, synthetic pseudoknots. #RNAsky #citsci Check out the puzzle at eternagame.org/labs/14333719

Third (& last?) intense week of #RNA server-only targets on #CASP17: small molecule binding ribozymes and aptamers & more group II introns in multiple states. Strange mix of natural and non-natural RNA and compounds and proteins. Looking forward to less crazy pace in next weeks.

The 2nd week of #CASP17 is closing, with more group II introns and some other RNAmake synthetic designs — the dimer targets for both kinds of targets seem challenging! And more #RNA targets are coming in week 3: predictioncenter.org/news.cgi#557

Latest #CASP17 #RNA targets are a tiny aptamer for tryptophan selected by Yarus lab @colorado.edu, a miniTTR by RNAmake @josephyesselman.bsky.social, and 2 singlet glycine riboswitches discovered by Breaker & Strobel labs. Note first one: 25-nt RNA by #cryoEM? predictioncenter.org/casp17/targe...

First natural #RNA in #CASP17 is a group II self-splicing intron, and it’s also the season's 1st multistate target! Will server algorithms detect homologous group II intron structures to help modeling? Can servers model both unspliced and spliced states? predictioncenter.org/casp17/targe...

More #CASP17 #RNA targets: OpenKnot @eternagame molecules from AI designers @rosettacommons.bsky.social @chaitjo.bsky.social & triphosphorylating ribozyme selected by Muller lab. All 8 RNA targets are non-natural — how will modeling methods do without MSAs, templates, homologous training examples?

First two targets in #CASP17 are #RNA, and they're designs from the online videogame @eternagame.org. Hope the bots preparing for CASP have been playing Eterna!

The 17th Critical Assessment of Structure Prediction #CASP17 begins tomorrow. 2 #RNA targets per day for next few weeks! >60 servers registered already, including @kaggle teams. Join the fun at predictioncenter.org/casp17/

Results are in for @stanfordmedicine.bsky.social Kaggle #RNA 3D Folding, Part 2! Top teams team_cp and AyPy together just outperform the best template oracle, another milestone in computational biology. Come join the conversation as we prepare for #CASP17: www.kaggle.com/c/stanford-r...

First public presentation of (Part 1 of) the #Kaggle 3D #RNA Folding challenge results -- see you Thursday!

Rachael Kretsch@rachael-kretsch.bsky.social · 8mo ago

Please join us for our next nucleic acid structure webinar, "Template-based RNA structure prediction advanced through a blind code competition," presented by Rhiju Das, G. John Rao, Toshiyuki Oda, Yehyun Kim, Raehyun Kim, Hyunkin Kim. Mailing list: groups.google.com/g/casp-rna-sig

In 2 weeks, 9 Kaggle teams have beat AlphaFold 3 score (0.372) in predicting hidden 3D structures of #RNA, including complexes with small molecules & proteins. What will it take to beat the best template oracle (0.554)? www.kaggle.com/c/stanford-r...

Large and intricate naturally occurring structures composed exclusively of RNA... ROOL! More at Molecule of the Month: pdb101.rcsb.org/motm...

Inspired by 2025 Stanford #RNA 3D folding @kaggle challenge outcome, we’ve collected cryo-EM of new-to-Nature RNA folds, RNA complexes with small molecules and proteins, and assemblies up to 6000 nts - and launched PART 2! Deadline: March 2026. www.kaggle.com/c/stanford-r...

Preprint on the Stanford #RNA 3D folding Kaggle challenge is out. My scientific new year’s resolution is to brush up on template-based modeling. #gofai www.biorxiv.org/content/10.6...

Template-based RNA structure prediction advanced through a blind code competition

Automatically predicting RNA 3D structure from sequence remains an unsolved challenge in biology and biotechnology. Here, we describe a Kaggle code competition engaging over 1700 teams and 43 previous...

biorxiv.org

A new 3-state Replicase challenge has been launched on Eterna and will only be open for two weeks before sequences are collected for experimental testing at the Das Lab. Will Eterna players be able to improve the catalytic activity of the RNA polymerase? eternagame.org/labs/14183416

Wonderful collab with Fu and Zuchero labs, led by @vedtopkar.bsky.social in our lab. How do molecules make it out to the myelin sheath? For the most expressed protein in oligodendrocytes, an #RNA switch appears to be the answer. Meng-meng's posts explain it best!

Meng-meng Fu@mengmengfu.bsky.social · 11mo ago

Excited to share our new pre-print collab w. @rdaslab.bsky.social Study led by Ved Topkar brilliant MD/PhD student who used biochemistry and bioinformatics to probe the relationship between Mbp mRNA structure & transport/local translation in oligodendrocytes! biorxiv.org/content/10.110… 1/8

@eternagame got single RNAs to compute functions like all logic gates, A>B, and A*B/C^2, relevant for tuberculosis detection! Now looking for partners to scale to complex applications. Collab w/ Greenleaf Khatri labs @christianchoe.bsky.social @stanfordmedicine.bsky.social at doi.org/10.1038/s415...

Compact RNA sensors for increasingly complex functions of multiple inputs - Nature Chemistry

Designing single molecules capable of complex sensing functions is challenging. Now, using crowdsourced RNA designs from the online game Eterna, compact single-molecule sensors have been demonstrated ...

doi.org

#MD blind predictions of water/ions around Tetrahymena ribozyme #RNA matched cryo-EM data better than our baselines! Congrats #CASP16 + @rachael-kretsch.bsky.social + 23 brave groups. Still a ways to go — time for #DeepLearning of water? Community paper: doi.org/10.1002/prot...

Our work presented today at the www.youtube.com/@CASPRNASIG online seminar! @bussigio.bsky.social will report on the #CASP16 solvation challenge and 2D ensemble reconstructions using #DMS data

CASP RNA SIG

Welcome nucleic acid enthusiasts to the Special Interest Group (SIG) focused different aspects of nucleic acid 3D structure prediction, including but not limited to obtaining experimental data, buildi...

youtube.com

Assessment of blind 3D structure modeling of #RNA and nucleic acid complexes now out in the #CASP16 special issue, led by @RachaelKretsch. We hope this benchmark, paper, metrics, and expert baselines drive much-needed progress by #CASP17 (May 2026)! doi.org/10.1002/prot...

The results are in: top codes in Stanford #RNA 3D Folding @kaggle.com competition are competitive with CASP16-leading humans Vfold, beat AlphaFold 3. Top team’s trick was template-based modeling, not #DeepLearning. Congrats: john, odat, Eigen, + all 1706 participants! www.kaggle.com/competitions...

Meet @frameshifter.org, the new nonprofit program established to steward Eterna's future and advance public engagement in scientific research through games, collective and hybrid intelligence, and human centered design.

Frameshifter@frameshifter.org · last yr.

Introducing: Frameshifter, a new nonprofit program (fiscally sponsored by @superbloom.design ) accelerating discoveries and inclusion in science through public engagement in research.

Community science presents an alternative discovery framework for precision ASO drugs. A community voting system facilitates the testing of top designs, followed by experimentation to evaluate and score how well player-designed drugs ameliorated molecular disease phenotypes bit.ly/44u5oTv

Highly collaborative efforts that involved 6 lab members and the labs of @yiliangding.bsky.social and @rdaslab.bsky.social. We uncovered a telomerase dimer and its potential role in telomere maintenance.

MRC Laboratory of Molecular Biology@mrclmb.ac.uk · last yr.

Sebastian Balch, Zala Sekne & Elsa Franco-Echevarría in @kellythd-nguyen.bsky.social's group have confirmed the existence of dimeric telomerase and illustrated how it is key to telomere maintenance: www2.mrc-lmb.cam.ac.uk/first-struct... #LMBResearch @yiliangding.bsky.social @rdaslab.bsky.social 🧪