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Das Lab

@rdaslab.bsky.social
105 followers 13 following 24 posts

Our lab seeks an agile and predictive understanding of how RNAs structurally code for information processing and replication in living systems.

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Das Lab @rdaslab.bsky.social · 27/08/2026
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...
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Das Lab @rdaslab.bsky.social · 18/08/2026
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
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Das Lab @rdaslab.bsky.social · 08/08/2026
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
eternagame.org
Eterna
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Das Lab @rdaslab.bsky.social · 25/07/2026
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...
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Reposted by Das Lab
Eterna @eternagame.org · 23/07/2026
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
Screenshot of the Eterna puzzle interface
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Das Lab @rdaslab.bsky.social · 14/07/2026
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
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Das Lab @rdaslab.bsky.social · 09/07/2026
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
eternagame.org
Eterna
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Das Lab @rdaslab.bsky.social · 15/05/2026
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.
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Das Lab @rdaslab.bsky.social · 09/05/2026
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
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Das Lab @rdaslab.bsky.social · 05/05/2026
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...
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Das Lab @rdaslab.bsky.social · 02/05/2026
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...
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Das Lab @rdaslab.bsky.social · 30/04/2026
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?
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Das Lab @rdaslab.bsky.social · 27/04/2026
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!
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Das Lab @rdaslab.bsky.social · 26/04/2026
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/
predictioncenter.org
Home - CASP17
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Das Lab @rdaslab.bsky.social · 31/03/2026
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...
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Das Lab @rdaslab.bsky.social · 03/02/2026
First public presentation of (Part 1 of) the #Kaggle 3D #RNA Folding challenge results -- see you Thursday!
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Das Lab @rdaslab.bsky.social · 24/01/2026
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...
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Reposted by Das Lab
RCSB Protein Data Bank @rcsbpdb.bsky.social · 05/01/2026
Large and intricate naturally occurring structures composed exclusively of RNA... ROOL! More at Molecule of the Month: pdb101.rcsb.org/motm...
OLE RNA from Clostridium botulinum (pdb_00009lcr) is shown in pink on the left. ROOL RNAs can form cages built from 6 (right, top, pdb_00009j6y) or 8 (right, bottom, pdb_00009mds) subunits.
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Das Lab @rdaslab.bsky.social · 08/01/2026
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...
kaggle.com
Stanford RNA 3D Folding Part 2
Solve RNA structure prediction, one of biology's remaining grand challenges
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Das Lab @rdaslab.bsky.social · 31/12/2025
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...
biorxiv.org
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...
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Reposted by Das Lab
Eterna @eternagame.org · 24/11/2025
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
The Eterna puzzle interface displaying the three states of the RNA polymerase ribozyme using RibonanzaNet in state 1 and Eternafold in states 2 and 3.
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Das Lab @rdaslab.bsky.social · 24/11/2025
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!
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Das Lab @rdaslab.bsky.social · 12/11/2025
@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...
doi.org
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 ...
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Das Lab @rdaslab.bsky.social · 11/11/2025
#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...
R1260 CASP target, water and ions around RNA. Ground truth on left, blind prediction from SoutheRNA MD simulations on right.
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Bussi Lab @bussilab.org · 30/10/2025
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
youtube.com
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...
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Das Lab @rdaslab.bsky.social · 30/10/2025
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...
Overlay of top blind model and cryo-EM structure for OLE RNA complex, only CASP16 RNA target showing strong improvements over prior templates
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Das Lab @rdaslab.bsky.social · 24/09/2025
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...
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Eterna @eternagame.org · 21/07/2025
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.
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RNA Society Journal @rnajournal.bsky.social · 16/07/2025
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
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Kelly Nguyen @kellythd-nguyen.bsky.social · 11/07/2025
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.
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