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]

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

[Das Lab @RDasLab]

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: https://t.co/Saawk3PpRQ

[Das Lab @RDasLab]

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? https://t.co/eHQ673sFm7

[Das Lab @RDasLab]

@ai4s_protenix Is Protenix-v1 AlphaFold-competitive for 3D #RNA structure prediction in the last and current Kaggle competitions? https://t.co/3SiTmewCQc https://t.co/CALoWmy3BB