Deni Szokoli
@szokoli.bsky.social
Ribozyme designer. Incoming postdoc at @rdaslab.bsky.social.
![4-panel comic. (1) [Three people. The person on the left has shoulder-length hair; the person on the right has a white hat.] PERSON 1: I’m sad that we missed the Perseids. PERSON 2 with hat: There’s still the Geminids. PERSON 1: Yeah, but they’re in December. (2) PERSON 1: The Perseids happen when it’s warm enough to lie outside with a blanket, and we found a good mosquito-free beach. So we just lie around watching the stars and eating snacks. One year we saw the aurora. (3) PERSON 3 with shoulder-length hair: You know, I think I heard that the Perseids might be late this year. PERSON 2: Yeah, actually, I heard that too. (4) Later… [Three people lying down gazing up at stars in dark sky. One meteor is in the sky.] PERSON 3: Hm, seems like a normal number of meteors. Guess I heard wrong. PERSON 1: Maybe the Perseids are *next* weekend. PERSON 2: Oh, good thinking. Let’s come back then, just in case.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreia2nfobiit5kmashzqken2545vvocu5wjnchfzw62yzvixksgunya)
On the citizen science platform Eterna, #AI methods matched expert human players at inventing sequences that fold into an RNA pseudoknot, a structure in which loops pair with distant parts of the same molecule. Learn more this week in Science: https://scim.ag/4wOqvuE
Our paper with @eternagame, 5 AI teams, and cryo-EM collabs on de novo design of #RNA pseudoknots with #deeplearning is out in @science.org! Comes with a provocative commentary on RNA structure prediction by @amustoe.bsky.social lab! doi.org/10.1126/scie... doi.org/10.1126/scie...
Jill Townley@jilltownley.bsky.social · last wk.How do researchers design an RNA in 3D when no accurate 3D prediction model exists? Eterna's collaboration with the @rdaslab.bsky.social at Stanford was able to design novel pseudoknots using a blend of secondary structure prediction and GenAI design methods. 🧪 #RNAsky
How do researchers design an RNA in 3D when no accurate 3D prediction model exists? Eterna's collaboration with the @rdaslab.bsky.social at Stanford was able to design novel pseudoknots using a blend of secondary structure prediction and GenAI design methods. 🧪 #RNAsky
Science Magazine@science.org · last wk.On the citizen science platform Eterna, #AI methods matched expert human players at inventing sequences that fold into an RNA pseudoknot, a structure in which loops pair with distant parts of the same molecule. Learn more this week in Science: https://scim.ag/4wOqvuE
Our new paper in PNAS reports the presence of Na+ and Li+ #aptamer RNAs in mammals. The latter hints at natural roles for #lithium in humans and provides direct links to #BipolarDisorder. Now seeking funding to study Li+ biology and create new therapeutics.
Finally, 3D #cryoEM structure of a nucleotide polymerizing #RNA that copies #RNA to #RNA: tC19z, evolved at @mrclmb.ac.uk 15 y ago! www.biorxiv.org/content/10.6... @szokoli.bsky.social Jason Hingey, Dan Haack, Vivian Wu Nick Spellmon @navtejtoor.bsky.social @hhmijanelia.bsky.social
We and @eternagame.org 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 eternagame.org/labs/14660266 by Aug 31, 2026! #RNAworld
Eterna
eternagame.org
Eterna@eternagame.org · 4w agoOur 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!
Can humans+AI get 1M #cryoEM-able #RNA structures? Phase 1: humans design 1000 pseudoknot structures @eternagame.org by Jul 19. Phase 2: AIs design 1000 sequences for each by Jul 31. Come join! Latest phase of the OpenKnot challenge eternagame.org/challenges/1... #citsci #RNAsky
Eterna
eternagame.org
Eterna@eternagame.org · 2mo agoEterna'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. #RNAsky #citsci Check out the puzzle at eternagame.org/labs/14333719
New! R-scape version v2.6.11 github.com/EddyRivasLab... with drawings of R-scape annotated RNA consensus structures with many fewer overlaps!! Using RFview github.com/dincarnato/R... Shout out to @incarnatolab.bsky.social for displaying R-scape's covariation outputs + CaCoFold-R3D structures.
Thrilled to be joining the ZMBH, where my lab will continue to explore the evolution and engineering of living membranes. Farewell @bcube-tud.bsky.social...I couldn't imagine a better place to have started my lab! I'm perpetually grateful to my lab group for making this such a successful adventure!!
ZMBH@zmbh.uni-heidelberg.de · 3mo agoThe ZMBH welcomes Dr. James Sáenz @jamessaenz.bsky.social as new Professor in Molecular Biology. James previously led a research group at B CUBE - Center for Molecular Bioengineering of Dresden University of Technology.
Conragtulations @ivanabukvin.bsky.social! 😁🥳
MRC Laboratory of Molecular Biology@mrclmb.ac.uk · 3mo agoThe LMB is thrilled to announce the appointment of @ivanabukvin.bsky.social as a Group Leader in the PNAC Division. Beginning in January 2027, Ivana’s group will investigate co-translational folding and misfolding of proteins. Read more: mrclmb.ac.uk/news-events/...
First AI-generated RNA with novel atomically ordered 3D fold! 🧬 The pseudoknotted secondary structure 'Kissing Multiloops' was designed by an Eterna player then solved by 3 GenAI models as confirmed by cryo-EM. ❄️🔬 #RNASky www.biorxiv.org/content/10.6...
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/targe...
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/
Home - CASP17
predictioncenter.org
I will probably be hiring either a PhD or a Postdoc in the near future. If you are interested in deep biochemical history or molecular mechanisms of evolution please get in touch.
Check out this incredible new method for the directed evolution of protein ON/OFF switches!!! www.cell.com/cell/fulltex...
Light-directed evolution of dynamic, multi-state, and computational protein functionalities
Optovolution leverages optogenetics and the yeast cell cycle to impose rapid, tunable selection, enabling the continuous evolution of light-responsive regulators, logic gates, and other complex protei...
cell.com
Looking for a truly unique PhD programme on RNA drugs and therapeutics? We have just opened the call for the second cohort of RNAmed-Future leaders in RNA-based medicine. More details under www.rnamed.de Please spread the word.
This is easily the most exciting ribozyme selection since the discovery of the Class I ligase! Must read!
Edoardo Gianni@edogia.bsky.social · 7mo agoHow could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in @science.org on a new small polymerase. 1/n
Engineering polymerases to synthesize alternative genetic polymers remains a challenge. Using DNA shuffling and droplet microfluidics, this study provides a short evolutionary path from a DNA polymerase to one with robust RNA-synthesizing activity www.nature.com/articles/s41...
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 2026. www.kaggle.com/c/stanford-r...
Stanford RNA 3D Folding Part 2
Solve RNA structure prediction, one of biology's remaining grand challenges
kaggle.com
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 www.biorxiv.org/content/10.6...
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 previous...
biorxiv.org
RNA switches designed by @eternagame.org players not only are highly efficient in vitro, they also work in cells! This is so cool! 🧪 @narjournal.bsky.social @markblenner.bsky.social Metabolite-responsive scaffold RNAs for dynamic CRISPR transcriptional regulation: academic.oup.com/nar/article/...
Metabolite-responsive scaffold RNAs for dynamic CRISPR transcriptional regulation
Abstract. CRISPR activation is a powerful tool to upregulate a vast array of genes in many different contexts. However, there are few dynamic CRISPR transc
academic.oup.com
✨New preprint! 🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al! Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬 🔗👇
This is incredible!
Chaitanya K. Joshi@chaitjo.bsky.social · 9mo agoIntroducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀 📝: tinyurl.com/gRNAde-paper Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
Really cool paper on the mechanism of group II intron folding. Will be very useful for RNA design in the future. www.nature.com/articles/s41...
Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy - Nature Communications
How RNA folds into functional structures is still largely uncharacterized. Here, using cryo-EM, SAXS, and molecular dynamics (MD) simulations, the authors create a movie of a medically relevant ribozy...
nature.com
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 the Das Lab. Will Eterna players be able to improve the catalytic activity of the RNA polymerase? eternagame.org/labs/14183416
🪱 Selfish genes are everywhere and drive some of biology’s biggest innovations (CRISPR, antibody recombination, epigenetics). Yet almost no one asks the obvious question: how does a selfish gene begin? Our new manuscript uncovers how selfishness can emerge directly from the host genome.
So happy to see this work out! Was such a pleasure to co-lead this effort with Erin. Do you like viral immune evasion, and using protein structure to study immune antagonists? Give it a read!
Erin Doherty@erinedoherty.bsky.social · 9mo agoWork I co-led with @jnoms.bsky.social is now online at @cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity. www.sciencedirect.com/science/arti...
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon. 🌐 evedesign.bio