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Reposted by Arne Schneuing

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · Sep 12

You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉

Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫

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Nature @nature.com · Sep 1

Nature research paper: One-shot design of functional protein binders with BindCraft

go.nature.com/46bhOAv

One-shot design of functional protein binders with BindCraft - Nature

BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.

go.nature.com

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Martin Pacesa @martinpacesa.bsky.social · Aug 27

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.

www.nature.com/articles/s41...

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Michael Bronstein @mmbronstein.bsky.social · Jul 24

@aithyra.bsky.social Opening Symposium "AI for Life Science" with Nobel Laureate Frances Arnold as keynote speaker in addition to an outstanding line up of speakers on a variety of topics across biological scales and data modalities.

Registration is now open at cemm.at/aithyra-symp...

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Frank Noe @franknoe.bsky.social · Jul 10

BioEmu now published in @science.org !!

What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...

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Arne Schneuing @rne.bsky.social · Jul 10

BioEmu is out! Grateful to have had the opportunity to work with such an incredible team on this project 🤗

Microsoft Research @msftresearch.bsky.social · Jul 10

Today in the journal Science: BioEmu from Microsoft Research AI for Science. This generative deep learning method emulates protein equilibrium ensembles – key for understanding protein function at scale. www.science.org/doi/10.1126/...

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Jose Jimenez-Luna @jjimenezluna.bsky.social · Jul 10

BioEmu is now on @science.org ! The revised version includes an upgraded model and makes a lot of MD simulation data internally generated at MSR available to the public. This took a lot of firepower from us in the last two years.
www.science.org/doi/10.1126/...

Scalable emulation of protein equilibrium ensembles with generative deep learning

Following the sequence and structure revolutions, predicting functionally relevant protein structure changes at scale remains an outstanding challenge. We introduce BioEmu, a deep learning system that...

www.science.org

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Science Magazine @science.org · Jul 3

New research in Science greatly expands the potential target scope of molecular glues and should stimulate the development of new small molecules that can selectively target therapeutically relevant proteins for degradation.

Learn more in this week's issue: scim.ag/44uRorm

This illustration shows the interface of the kinase NEK7 (light blue) and the E3 ubiquitin ligase substrate receptor cereblon (teal). The interaction is facilitated by the small molecule MRT-3486 (orange).

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Martin Pacesa @martinpacesa.bsky.social · Jun 30

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!

github.com/martinpacesa...

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AITHYRA Research Institute of the Austrian Academy of Sciences @aithyra.bsky.social · Apr 28

Please welcome AITHYRA, the Research Institute for Artificial Intelligence of the Austrian Academy of Science on social media. Follow us and connect via Bluesky and LinkedIn 👋

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Rebecca Neeser @rebeccaneeser.bsky.social · Apr 24

Hello from Singapore 🇸🇬! Thrilled to be at #ICLR2025 presenting our work on fragment-based drug discovery 🧩. We go beyond virtual screening with a generative, structure-aware approach.

📃 openreview.net/forum?id=bZW... 
🔗 github.com/rneeser/Late...

A thread 🧵👇

Flow-Based Fragment Identification via Contrastive Learning of...

Fragment-based drug design is a promising strategy leveraging the binding of individual fragments, potentially yielding ligands with multiple key interactions, surpassing the efficiency of full...

openreview.net

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Michael Bronstein @mmbronstein.bsky.social · Apr 21

Come to see our papers at #ICLR2025 in Singapore

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Damiano Sgarbossa @damianosg.bsky.social · Apr 11

📢 Our new preprint is out on bioRxiv! We introduce RAG-ESM, a retrieval-augmented framework that improves pretrained protein language models like ESM2 by making them homology-aware with minimal additional training costs.
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...

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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Mar 29

Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations.
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...

Google Colab

colab.research.google.com

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Leo Scheller @leoscheller.bsky.social · Mar 13

I’m looking for a BTA and a Postdoc to help set up the Structural Biochemistry group at the Leibniz Institute for Immunotherapy (LIT) in Regensburg 😀.

We apply synthetic biology and protein design to address key challenges in immunotherapy.
lit.eu/work-with-us/
#SynBio #ProteinDesign #Immunotherapy

Work With Us

The LIT welcomes individuals from all life paths and academic backgrounds. If you are passionate about science we could be the perfect home for you.

lit.eu

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Ilia Igashov @igashov.bsky.social · Mar 11

🚨 Check out DrugFlow, our new generative model for structure-based drug design. DrugFlow provides an atom-level confidence score for each designed molecule, and can adjust molecular size on the fly!

Additional details in thread 🧵

#ICLR2025

Arne Schneuing @rne.bsky.social · Mar 7

The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available

📚 Paper: openreview.net/forum?id=g3V...

💻 Code: github.com/LPDI-EPFL/Dr...

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Chaitanya K. Joshi @chaitjo.bsky.social · Mar 10

Introducing All-atom Diffusion Transformers

— towards Foundation Models for generative chemistry, from my internship with the FAIR Chemistry team

There are a couple ML ideas which I think are new and exciting in here 👇

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Arne Schneuing @rne.bsky.social · Mar 7

For benchmarking, we placed a lot of emphasis on distribution learning capabilities because this reflects the training objective of generative models. But we also show how downstream preference optimization can be used to further improve molecular properties.

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Arne Schneuing @rne.bsky.social · Mar 7

These models are equipped with a few new features including:

1. protein side chain modeling
2. adaptive ligand sizes
3. confidence score
4. preference alignment

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Arne Schneuing @rne.bsky.social · Mar 7

We (together with @igashov.bsky.social, @adobbelstein.bsky.social, Thomas, @mmbronstein.bsky.social, and Bruno) introduce two new models for target-conditioned drug design in 3D (DrugFlow and FlexFlow), which sample new molecules using a mixed continuous/discrete generative framework.

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Arne Schneuing @rne.bsky.social · Mar 7

The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available

📚 Paper: openreview.net/forum?id=g3V...

💻 Code: github.com/LPDI-EPFL/Dr...

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Frank Noe @franknoe.bsky.social · Feb 19

The BioEmu-1 model and inference code are now public under MIT license!!!

Please go ahead, play with it and let us know if there are issues.

github.com/microsoft/bi...

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Martin Pacesa @martinpacesa.bsky.social · Jan 19

We processed the results of the BindCraft user experience poll and we are quite happy with how it turned out. We had over 60 responses from many different users, turns about about a quarter are from industry and a quarter of users run it via Google Colab!

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Arne Schneuing @rne.bsky.social · Jan 15

Compared to the preprint (biorxiv.org/content/10.1...), we added an optimised design pipeline using AlphaFold and LigandMPNN, and super cool tumour cell killing results from Maddalena.

Targeting protein-ligand neosurfaces using a generalizable deep learning approach

Molecular recognition events between proteins drive biological processes in living systems. However, higher levels of mechanistic regulation have emerged, where protein-protein interactions are condit...

biorxiv.org

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Arne Schneuing @rne.bsky.social · Jan 15

Our paper on computational design of chemically induced protein interactions is out in @natureportfolio.bsky.social. Big thanks to all co-authors, especially Anthony Marchand, Stephen Buckley and Bruno Correia!

t.co/vtYlhi8aQm

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