Our lab seeks an agile and predictive understanding of how RNAs structurally code for information processing and replication in living systems.
Joined April 2019
- Tweets 254
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50 Photos and videos
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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The 2nd week of #CASP17 is closing, with more group II introns and some other RNAmake synthetic designs — monomer and dimer (!) targets for both. And more #RNA targets are coming in week 3: predictioncenter.org/news.cg…
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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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First two targets in #CASP17 are #RNA, and they're designs from the online videogame @eternagame. Hope the bots preparing for CASP have been playing Eterna!
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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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First public presentation of (Part 1 of) the @kaggle 3D RNA Folding challenge results -- see you Thursday!
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…
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It's official: @NVIDIAHealth has returned to co-organize Part 2 of the @StanfordMed Kaggle 3D RNA folding competition. Kagglers incl Part 1 leader @raojohng have already advanced @nvidia RNApro into the best publicly available notebook on the leaderboard: kaggle.com/competitions/stan…
Jan 27
🧩 We’re thrilled to collaborate with @StanfordMed and @HHMIJanelia on the Stanford RNA 3D Folding Part 2 Challenge.
Help advance the science of RNA structure prediction and push the boundaries of AI for biology.
Kickstart your solution with RNAPro, our new baseline model built on key insights from the first competition.
🤔 Can you solve it nvda.ws/4q0FRsw
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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)? kaggle.com/c/stanford-rna-3d…
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Awesome to work with @NVIDIAHealth @kaggle teams on pushing RNA structure prediction with the RNApro model – come join us in next steps at kaggle.com/c/stanford-rna-3d…
Jan 15
👩💻 Try it out today nvda.ws/3LPQCQt
📄 Read the preprint nvda.ws/4jFkCek
📣 Check out the next iteration of this competition nvda.ws/3NLW6MB
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Das Lab retweeted
First Molecule of the Month of 2026: Natural RNA-Only Assemblies
pdb101.rcsb.org/motm/313
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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 19, 2026. kaggle.com/c/stanford-rna-3d…
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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
biorxiv.org/content/10.64898…
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Das Lab retweeted
27 Nov 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 @RDasLab. Will Eterna players be able to improve the catalytic activity of the RNA polymerase?
eternagame.org/labs/14183416
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Wonderful collab with Fu and Zuchero labs, led by @vedtopkar 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!
24 Nov 2025
Excited to share our new pre-print collab w. @RDasLab!
Study led by @VedTopkar 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/10.1101/…
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