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Das Lab @RDasLab

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

Joined April 2019
  • Posts 254
  • Following 103
  • Followers 2,676
50 Photos and videos
Das Lab @RDasLab
May 23
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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Das Lab @RDasLab
May 15
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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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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Das Lab @RDasLab
Apr 30
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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Das Lab @RDasLab
Apr 29
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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Das Lab @RDasLab
Apr 27
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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Das Lab @RDasLab
Apr 26
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/
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Das Lab @RDasLab
Mar 31
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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Das Lab @RDasLab
Feb 27
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!
Rachael Kretsch @RachaelKretsch
Feb 3
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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Das Lab @RDasLab
Jan 27
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…

Stanford RNA 3D Folding Part 2

Solve RNA structure prediction, one of biology's remaining grand challenges

kaggle.com
NVIDIA Healthcare
 @NVIDIAHealth
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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Das Lab @RDasLab
Jan 24
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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Das Lab @RDasLab
Jan 16
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…

Stanford RNA 3D Folding Part 2

Solve RNA structure prediction, one of biology's remaining grand challenges

kaggle.com
NVIDIA Healthcare
 @NVIDIAHealth
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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First Molecule of the Month of 2026: Natural RNA-Only Assemblies pdb101.rcsb.org/motm/313

PDB101: Molecule of the Month: Natural RNA-Only Assemblies

Large and intricate naturally occurring structures composed exclusively of RNA

pdb101.rcsb.org
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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…

Stanford RNA 3D Folding Part 2

Solve RNA structure prediction, one of biology's remaining grand challenges

kaggle.com
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Das Lab @RDasLab
31 Dec 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 biorxiv.org/content/10.64898…

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...

biorxiv.org
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Das Lab reposted
Eterna @eternagame
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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Das Lab @RDasLab
24 Nov 2025
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!
Meng-meng Fu @Meng2Fu
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/… 1/8
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