Arne Schneuing

Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!

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💫

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.

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

go.nature.com/46bhOAv

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...

@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...

BioEmu now published in @science.org !!

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

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

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...

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/...

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).

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

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...

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 👋

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...

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 🧵👇

Come to see our papers at #ICLR2025 in Singapore

RAG-ESM logo

📢 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...

1/7

Google Colab

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...

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.

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

🚨 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

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 👇

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.

(4/4)

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

(3/4)

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.

(2/4)

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...

(1/4)

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...

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!

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...

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.

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

Awesome paper!
BioEmu from MSR: Scalable emulation of protein equilibrium ensembles with generative deep learning www.biorxiv.org/content/10.1...

Looking forward to hearing more explanainers in tomorrow's reading group session on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg

Structure-based drug design with equivariant diffusion models - Nature Computational Science This work applies diffusion models to conditional molecule generation and shows how they can be used to tackle various structure-based drug design problems

After two years, our paper on generative models for structure-based drug design is finally out in @natcomputsci.bsky.social

www.nature.com/articles/s43...

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...

@rebeccaneeser.bsky.social @damianosg.bsky.social @pschwllr.bsky.social