ginaelnesr.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Today we have published BioEmu-Benchmarks (MIT license): a code to evaluate the multi-conformation sampling benchmarks, MD free energy landscape benchmarks, and folding free energy benchmarks shown in the BioEmu-1 paper with BioEmu or your own model. Some details below 🧵 github.com/microsoft/bi...

submitted 5 days ago • 4 comments

We made a new, reproducible, fair, (and much harder) motif scaffolding benchmark! Paper: arxiv.org/abs/2502.12479 Code: github.com/blt2114/Moti...

submitted 7 days ago • 2 comments

🔥 Benchmark Alert! MotifBench sets a new standard for evaluating protein design methods in motif scaffolding. Why does this matter? Reproducibility & fair comparison have been lacking—until now. Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti... A thread ⬇️

submitted 7 days ago • 1 comment

Excited to share our new AllMetal3D model building on Metal3D. AllMetal3D predicts the location, identity and geometry of the major biologically relevant metal ions doi.org/10.1101/2025...

submitted 17 days ago • 1 comment

🧬🧪Protein codes promote selective subcellular compartmentalization | Science www.science.org/doi/10.1126/... Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social

submitted 18 days ago • 3 comments

"My memories of Lebanon and the resilience of its people strengthened my resolve." This week's #ScienceWorkingLife: https://scim.ag/3C2dtnd

submitted 37 days ago • 0 comments

Bluetorial: Metal regulation, an unexpected connection, and a deep evolutionary insight

submitted 57 days ago • 3 comments

Hi Bluesky, just in time for the holidays I am excited to share the latest pre-print from my group! We solved the 3D structure of a mysterious viral RNA that resists degradation by host nucleases. A short 🧵 &link below – please also check out the full video! #RNA #RNAbiology #RNASky #lovevirology

submitted 68 days ago • 8 comments

A periodic reminder that biologically meaningful conformational changes do not have to be large While textbooks may indicate that relevant motions are large, even the original paper on alternating access makes it clear that atoms just need to move a bit to have an effect. doi.org/10.1038/2119... 🧬🧶

submitted 72 days ago • 6 comments

Incredible work from Haotian and Jingjia using a de novo protein platform called TRACeR for high specificity targeting of MHC-I and MHC-II antigens Two papers, both worth the read ⬇️

submitted 72 days ago • 0 comments

A new system, TRACeR-I, targets peptides on MHC I molecules with high precision, enabling specific tumor and virus cell killing. It powers CAR-T and BiTE therapies, showing potential to transform cancer and infectious disease treatment. www.nature.com/articles/s41...

submitted 73 days ago • 0 comments

1/ In two back-to-back papers, we present our de novo TRACeR platform for targeting MHC-I and MHC-II antigens TRACeR for MHC-I: go.nature.com/4gcLzn5 TRACeR for MHC-II: go.nature.com/4gj5OQk

submitted 72 days ago • 2 comments

a good benchmark only cost me 22 CAD

submitted 72 days ago • 0 comments

thank you to everyone who came to @workshopmlsb.bsky.social!!! more so, thank you Erika Alden DeBenedictis for the fire crowd-sourced brainstorming 🔥🔥🔥

submitted 73 days ago • 0 comments

MLSB happening today! Packed room at @neuripsconf.bsky.social East Building Rm 11-12 @workshopmlsb.bsky.social

submitted 73 days ago • 0 comments

Predicting absolute protein folding stability using generative models @mcagiada.bsky.social @sokrypton.org & I used ESM-IF to predict ∆G for folding & conformational change Paper, code and colab 📜 dx.doi.org/10.1002/pro.... 💾 github.com/KULL-Centre/... 👩‍💻 colab.research.google.com/github/KULL-...

submitted 74 days ago • 1 comment

We discovered 3 RNA families that form homo-oligomeric RNA-only complexes! Studying nature continues to expand my wildest imagination. Read about it: doi.org/10.1101/2024... Vivian Wu, Svetlana Shabalina, Hyunbin Lee, Grace Nye, Eugene Koonin, Alex Gao, Rhiju Das, Wah Chiu

submitted 76 days ago • 3 comments

Naturally ornate RNA-only complexes revealed by cryo-EM https://www.biorxiv.org/content/10.1101/2024.12.08.627333v1

submitted 79 days ago • 2 comments

The more I think about it, the more convinced I am that the holy grail here is if this can go beyond predicting ratio of folded to unfolded, to also predicting ratio of folded state A to folded states B, C, D, etc. Example from doi.org/10.1016/j.molcel.2024.04.008 w/ changes in the transporter OCT1

submitted 78 days ago • 4 comments

Really beautiful RNA structures from Rachel Kretsch in the Das and Chiu groups These look like viral capsids but they're only RNA!! Hopefully this unlocks more work on "ornate" RNAs 🧪 www.biorxiv.org/content/10.1...

submitted 78 days ago • 3 comments

Both PLINDER and PINDER datasets are supported!

submitted 79 days ago • 0 comments

Re docking: @workshopmlsb.bsky.social has been piloting a leaderboard for the PLINDER benchmark. It would be awesome to get submissions using existing methods, then everyone can see comparisons better 😁 leaderboard & instructions are on mlsb.io

submitted 79 days ago • 1 comment

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

submitted 83 days ago • 22 comments

Introducing ESM Cambrian, a new family of protein language models, focused on creating representations of the underlying biology of proteins.

submitted 84 days ago • 1 comment

Also from the GitHub repo: antibody antigen docking performance comparison to Boltz-1 and AF-2.3

submitted 90 days ago • 0 comments

Fascinating thread here: apparently, caffeine and ibuprofen both have binding affinity to their target proteins so weak that they might get tossed out of a typical drug discovery project!

submitted 92 days ago • 1 comment

Theodor W. Hänsch, from his Nobel lecture in 2005 (www.nobelprize.org/prizes/physi... Curiosity-driven research vs goal-oriented research

submitted 92 days ago • 2 comments

what a pleasure to have been a guest editor alongside @hkws.bsky.social and @gcorso.bsky.social. We are really excited by this new collection showcasing ML in structural biology!

submitted 97 days ago • 0 comments

This past year, the organizers at @workshopmlsb.bsky.social partnered with PRX Life to create a special collection focused on the topic of "machine learning in structural biology". Was a pleasure to work together trying to create a venue for workshop papers! journals.aps.org/prxlife/abst...

submitted 97 days ago • 1 comment

#GoodThingsComeToThoseWait Sorry it's taking us a while. Promise that the wait will be well worth it! #OpenFold3 Love all the great work that's already been done #HelixFold3 #Ligo #Chai1 #Protenix #Boltz1

submitted 98 days ago • 3 comments

MLSB workshop is now on Bluesky!

submitted 100 days ago • 0 comments

hello world! find me in starter pack 1, excited to be on the 🦋app!

submitted 100 days ago • 0 comments

Here are some free/open-source sites for the preparation of scientific illustrations, including icon libraries: bioicons.com, scidraw.io, bioart.niaid.nih.gov, inkscape.org, biogdp.com, reactome.org/icon-lib

submitted 101 days ago • 59 comments

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!

submitted 101 days ago • 18 comments

New at Science Evo, a large language of life (LLLM) genomic foundation model, predicting & generating tasks from molecular to genomic scale science.org/doi/10.1126/...

submitted 104 days ago • 3 comments

Another protein structure diffusion paper just got published and once again, the presented method runs into trouble with beta-sheets (sequence design via ProteinMPNN), frequently failing to reach a generous scTM-score cutoff of 0.5 doi.org/10.1038/s41467-024-45051-2

submitted 387 days ago • 1 comment