Das Lab

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

[Das Lab @RDasLab]

Has there been progress in 3D #RNA structure modeling? #CASP17 conference will be on December 1-6 this year. See you in Rome!

[Das Lab @RDasLab]

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! https://t.co/UuwyK18qdU https://t.co/jtNjJPe0Ir

[Eterna @eternagame]

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.

[Das Lab @RDasLab]

Finally, 3D #cryoEM structure of a nucleotide polymerizing #RNA that copies #RNA to #RNA: tC19z, evolved at LMB MRC 15 y ago! https://t.co/bepvYcE32z @Szokoli_Deni Jason Hingey, Dan Haack, Vivian Wu @nickspellmon @navtejtoor @HHMIJanelia

[Das Lab @RDasLab]

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 https://t.co/dDCM1KVNe0 by Aug 31, 2026! #RNAworld

[Eterna @eternagame]

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!

[Das Lab @RDasLab]

#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.

[Eterna @eternagame]

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.

[Das Lab @RDasLab]

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:
https://t.co/MKCLtTAKL1

[Eterna @eternagame]

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: https://t.co/SWgjl7iAIO

[Das Lab @RDasLab]

Pseudoknots, AI, and preview of Eterna's first RNA replicase results at EternaCon 12, virtual on Sunday July 26, 2026! Preregister for free at: https://t.co/ZldsaMtkIt

[Das Lab @RDasLab]

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 https://t.co/uhjuZFCMYX

[Eterna @eternagame]

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 https://t.co/a1fN0uupjT

[Das Lab @RDasLab]

Our lab is very honored to be recognized with Stanford's Open Science Champion Prize https://t.co/oX3wL2ulvf for efforts including @eternagame. Thanks for supporting an extraordinary community @StanfordData @StanfordHAI!

[Das Lab @RDasLab]

@lisaeshunwilson @eternagame @StanfordBiochem @chaitjo @PossuHuangLab @UWproteindesign @ShujunHe0717 @navtejtoor @HHMIJanelia Good question! Another AI-generated molecule in the study formed a dimer unexpectedly. But we haven't found or designed any more super-elaborate oligomers like the natural assemblies discovered last year (https://t.co/2bpVVK4t60).

[Das Lab @RDasLab]

First AI-generated RNA with novel atomically ordered 3D fold! With @eternagame @StanfordBiochem @chaitjo @PossuHuangLab @UWproteindesign @ShujunHe0717 @navtejtoor @HHMIJanelia on bioRxiv https://t.co/rO8OVU1Avd

[Das Lab @RDasLab]

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.

[Das Lab @RDasLab]

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: https://t.co/sVz2D7wOJc

[Das Lab @RDasLab]

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? https://t.co/r9IAvhN28g

[Das Lab @RDasLab]

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? https://t.co/r9IAvhN28g

[Das Lab @RDasLab]

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?

[Das Lab @RDasLab]

Next four #CASP17 #RNA targets are another @eternagame OpenKnot design and computational RNA designs from 3 distinct deep learning methods by @ShujunHe0717 @UWproteindesign! https://t.co/r9IAvhN28g

[Das Lab @RDasLab]

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!

[Das Lab @RDasLab]

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 https://t.co/wbMGUMryza