Das Lab

243 posts

Das Lab

@RDasLab

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

Stanford, CA Katılım Nisan 2019

111 Takip Edilen2.5K Takipçiler

Das Lab@RDasLab·27 Şub

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…

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Das Lab@RDasLab·5 Şub

@ai4s_protenix Is Protenix-v1 AlphaFold-competitive for 3D #RNA structure prediction in the last and current Kaggle competitions? kaggle.com/competitions/s… kaggle.com/competitions/s…

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Protenix@ai4s_protenix·4 Şub

🚀 Introducing Protenix-v1, the first open-source model achieving AF3-level performance Highlights: 🔹 Verified inference-time scaling behavior 🔹 RNA MSA & protein template support 🔹 Additional release: Protenix-v1-20250630 trained on a larger dataset 🔹 PXMeter v1.0.0 for transparent evaluation (6k+ complexes, time-split & domain-specific subsets) 🔗 Code: github.com/bytedance/Prot… 🔗 Eval toolkit: github.com/bytedance/PXMe… 🔗 Online server: protenix-server.com

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Das Lab@RDasLab·3 Şub

First public presentation of (Part 1 of) the @kaggle 3D RNA Folding challenge results -- see you Thursday!

Rachael Kretsch@RachaelKretsch

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-sig

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Das Lab@RDasLab·27 Oca

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/s…

NVIDIA Healthcare@NVIDIAHealth

🧩 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·25 Oca

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…

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Das Lab@RDasLab·16 Oca

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…

NVIDIA Healthcare@NVIDIAHealth

👩‍💻 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 retweetledi

rcsb pdb 💉🧬💻🔬💊🌱🧠🦠@buildmodels·2 Oca

First Molecule of the Month of 2026: Natural RNA-Only Assemblies pdb101.rcsb.org/motm/313

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Das Lab@RDasLab·8 Oca

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…

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Das Lab@RDasLab·31 Ara

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/10.648…

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Das Lab retweetledi

Eterna@eternagame·27 Kas

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 Kas

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

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/10.110… 1/8

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Das Lab retweetledi

Meng-meng Fu@Meng2Fu·24 Kas

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Das Lab@RDasLab·13 Kas

We got single RNAs to compute functions like all logic gates, A>B, and A*B/C^2, relevant for tuberculosis detection! Now looking for partners to scale to complex applications. Awesome collaboration with @WJGreenleaf @purveshkhatri @eternagame at doi.org/10.1038/s41557…

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Das Lab@RDasLab·11 Kas

#MD blind predictions of water/ions around Tetrahymena ribozyme #RNA matched cryo-EM data better than our baselines! Congrats #CASP16 + @RachaelKretsch+ 23 brave groups. Still a ways to go — time for #DeepLearning of water? Community paper: doi.org/10.1002/prot.7…

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Das Lab@RDasLab·30 Eki

Assessment of blind 3D structure modeling of #RNA and nucleic acid complexes now out in the #CASP16 special issue, led by @RachaelKretsch. We hope this benchmark, paper, metrics, and expert baselines drive much-needed progress by #CASP17 (May 2026)! doi.org/10.1002/prot.7…

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Das Lab@RDasLab·24 Eyl

The results are in: top codes in Stanford #RNA 3D Folding @kaggle are competitive with CASP16-leading humans Vfold, beat AlphaFold 3. Top team’s trick was template-based modeling, not #DeepLearning. Congrats: john, odat, Eigen, + all 1706 participants! kaggle.com/competitions/s…

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Das Lab@RDasLab·2 Haz

Nice overview in @naturemethods of #RNA structure approaches featuring our very own @RachaelKretsch and lots of amazing colleagues across the world nature.com/articles/s4159…

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Das Lab@RDasLab·30 May

At Final Submission Deadline, numerous @kaggle notebooks outperform VFold human expert baseline in #RNA 3D structure prediction! Will these codes sustain performance on new targets released between now and Sep 2025? Join the discussion: kaggle.com/competitions/s…

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Das Lab@RDasLab·11 May

#RNA 3D structure prediction remains an open problem! Come test new ideas against SOTA & >1000 teams in Kaggle RNA 3D Folding competition, co-hosted by #CASP16 and @rnapuzzles, 2.5 weeks left. kaggle.com/competitions/s… N/N

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Das Lab@RDasLab·11 May

Nucleic acid assessment for #CASP16 blind competition is out. As in prior challenges #deeplearning for 3D #RNA structure in #CASP16 prediction remains disappointing. doi.org/10.1101/2025.0… 1/N

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Das Lab@RDasLab·11 May

#CASP16 enabled by 46 predictor labs, 22 experimental #RNA and #DNA groups, co-assessors @rachaelkretsch, @alissahummer, @ShujunHe0717, @RongqingY, Jing Zhang, Thomas Karagianes, @qiancong, @AKryshtafovych Many thanks! 7/N

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Keşfet

@kaggle @ai4s_protenix @NVIDIAHealth @StanfordMed @raojohng @nvidia @VedTopkar @WJGreenleaf