Our lab seeks an agile and predictive understanding of how RNAs structurally code for information processing and replication in living systems.
Stanford, CA
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Our paper with @eternagame, 5 AI teams, and cryo-EM collabs on de novo design of #RNA pseudoknots with #deeplearning is out in @ScienceMagazine ! Comes with a provocative commentary on RNA structure prediction by @TonyMustoe lab! doi.org/10.1126/science.aeg6… doi.org/10.1126/science.aek4…
We made the cover of Science! Congratulations to all the players and researchers who worked so hard on the OpenKnot project the last two years.
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Finally, 3D #cryoEM structure of a nucleotide polymerizing #RNA that copies #RNA to #RNA: tC19z, evolved at LMB MRC 15 y ago! biorxiv.org/content/10.64898… @Szokoli_Deni Jason Hingey, Dan Haack, Vivian Wu @nickspellmon @navtejtoor @HHMIJanelia
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We and @eternagame 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
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!
ALT Puzzle interface displaying both the secondary and tertiary structure of the ribozyme
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#RNA computational design groups around the world delivered! Congrats as well to @eternagame players who contributed the 240-nt pseudoknot targets -- and baseline RNA sequences for #AI eval. Experiments are underway at @StanfordBiochem @HHMI Janelia Research Campus.
Major props @DidiKieran @jgkoob @lemerleau @IIMCB_Poland @FrankRHutter @AF_Panescu @chaitjo @rishabh16_ for generating 600,000 sequences to fold into 1000 synthetic pseudoknots! The wet lab results will help these researchers improve their computational methods for RNA design.
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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/…
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Das Lab retweeted
OpenKnot Round 9 features secondary structures designed by players to create compact, pseudoknotted RNA using 240 bases. GenAI teams also will test whether their methods perform as well as the expert players at a longer length.
Check out the puzzle at: eternagame.org/labs/14343053
ALT Screenshot of Eterna puzzle interface
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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/202…
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Can humans+AI get 1M #cryoEM-able #RNA structures?
Phase 1: humans design 1000 pseudoknot structures @eternagame 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/11…
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.
Check out the puzzle at eternagame.org/labs/14333719
ALT ZG_25 by Father_Z
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Our lab is very honored to be recognized with Stanford's Open Science Champion Prize datascience.stanford.edu/cor… for efforts including @eternagame. Thanks for supporting an extraordinary community @StanfordData @StanfordHAI!
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First AI-generated RNA with novel atomically ordered 3D fold! With @eternagame @StanfordBiochem @chaitjo @PossuHuangLab @UWproteindesign @ShujunHe0717 @navtejtoor @HHMIJanelia on bioRxiv doi.org/10.64898/2026.05.21.…
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Latest #CASP17 #RNA targets are a tiny aptamer for tryptophan selected by Yarus lab @cuboulder, a miniTTR by RNAmake @JosephYesselman, and two singlet glycine riboswitches discovered by @ronbreaker Strobel. Note that first one — a 25-nt RNA by #cryoEM? predictioncenter.org/casp17/…
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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/…
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Two more #CASP17 #RNA targets: OpenKnot @eternagame molecule from AI designer gRNAde @chaitjo & triphosphorylating ribozyme selected by Muller lab @UCSanDiego. All 8 RNA targets are non-natural — how will modeling methods do without MSAs, templates, homologous training examples?
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Next four #CASP17 #RNA targets are another @eternagame OpenKnot design and computational RNA designs from 3 distinct deep learning methods by @ShujunHe0717 @UWproteindesign! predictioncenter.org/casp17/…
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Results are in for @StanfordMed @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: kaggle.com/c/stanford-rna-3d…
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Best codes in Stanford @kaggle #RNA 3D Folding challenge are getting better after release of protenix-v1 @ai4s_protenix and RNApro @NvidiaHealth. No apparent impact from Agentic AI yet. Can any team or agent beat the best template oracle by March? kaggle.com/c/stanford-rna-3d…
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