Vincent Voelz

Excited to be a part of this review paper by Chapin Cavender et al. Now out in LiveCoMS! doi.org/10.33011/liv...

A brief introduction to HADDOCK3 — haddock3 3.0.0 documentation HADDOCK3 is the next generation integrative modelling software in the long-lasting HADDOCK project. It represents a complete rethinking and rewriting of the HADDOCK2.X series, implementing a new way…

New Title Alert: HADDOCK3- is the next generation integrative modeling software in the long-lasting HADDOCK project.

Learn more here: buff.ly/gInH6VV

#SBGrid #SBGridSoftware #StructuralBiology

Philadelphia Freedom. 🇺🇸 #NoKings

Structures from AlphaFold3 - while often impressively good - tend to fail representing the dynamic ensembles accurately. And often parts of the structure are not correct. Adding experimental data, directly in AlphaFold's diffusion step, provides physically realistic protein ensembles. This image shows two cases where AlphaFold3-only structures were largely improved by guiding with experimental data.

📢 New preprint:
Experiment-guided AlphaFold3 resolves accurate protein ensembles.
doi.org/10.1101/2025...

AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇

Embracing the avoid-ome Patrick Walters, the chief scientist of OpenADMET, discusses an ambitious open-science project aimed at figuring out how to avoid pharmacokinetic and toxicity traps in small-molecule drug discovery.

Could not be more thrilled to have Pat Walters (@wpwalters.bsky.social) at the scientific helm of OpenADMET!m (@openadmet.bsky.social)! 🎉

Check out this new interview with Pat in Nature Reviews Drug Discovery:
www.nature.com/articles/d41...

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

Mapping the diverse topologies of protein-protein interaction fitness landscapes De novo binder discovery is unpredictable and inefficient due to a lack of quantitative understanding of protein-protein interaction (PPI) sequence-function landscapes. Here, we use our PANCS-Binder t...

Our latest work seeks to answer a longstanding question: why is discovering new protein binders seemingly unpredictable – and can we better quantify and understand the de novo binder discover process? 1/12

www.biorxiv.org/content/10.1...

Resolving Molecular Interactions in Protein Folding Trajectories with NCIPLOT Noncovalent interactions (NCIs) are fundamental to the structure, stability, and function of proteins. These interactions form complex networks that control how different protein regions relate to eac...

Out in its final form
pubs.acs.org/doi/10.1021/...

YouTube video by ProteinDesignStudio Screen binders using ipSAE

pip install ipsae
from www.linkedin.com/in/ullah-sam...

www.youtube.com/watch?v=A5ph...
PyPI pypi.org/project/ipsae/
His github fork github.com/ullahsamee/I...
My github github.com/DunbrackLab/...
Paper www.biorxiv.org/content/10.1...
For designed protein binders www.biorxiv.org/content/10.1...

Brought to you by Austin Cheng (@auhcheng.bsky.social) — meet the newest member of our team: Quetzal!

Named after Quetzalcoatl, the Aztec god of creation, Quetzal is a simple yet scalable model for building 3D molecules atom by atom.

📜 arxiv.org/abs/2505.13791

[1/4]

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...

New preprint: www.biorxiv.org/content/10.1...
We used molecular dynamics simulations and solid-state NMR (@fmp-berlin.de) to look at calcium binding to the pore domain of the calcium-gated K+ channel MthK. @wojciechkopec.bsky.social @compbiophys.bsky.social

Massively Parallel Free Energy Calculations for In Silico Affinity Maturation of Designed Miniproteins Computational protein design efforts continue to make remarkable advances, yet the discovery of high-affinity binders typically requires large-scale experimental screening of site-saturated mutant (SS...

Excited to share the final paper from my PhD in @voelzlab.bsky.social , out now in #JCTC @acs.org ! We ran ~43k expanded ensemble free energy calculations on @foldingathome.org to do in silico site saturation mutagenesis on designed hemagglutinin minibinder proteins.

🔗 doi.org/10.1021/acs....

ACS announces 2026 national award winners The winners are being acknowledged for their outstanding achievements in chemistry across various fields in the discipline

ACS announces 2026 national award winners

The winners are being acknowledged for their outstanding achievements in chemistry across various fields in the discipline. cen.acs.org/people/award...

CACHE 7 is launched with support from the @gatesfoundation.bsky.social and unpublished data from Damian Young at @bcmhouston.bsky.social, Tim Willson @thesgc.bsky.social and Neelagandan Kamaria InSTEM. Design selective PGK2 inhibitors. We'll test them experimentally.
bit.ly/4lnVYOs

We are delighted to announce that our perspective article, “Steering towards safe self-driving laboratories (SDLs),” has been accepted for publication in Nature Reviews Chemistry.

Link: www.nature.com/articles/s41...

Alpha-synuclein interacts with regulators of ATP homeostasis in mitochondria - Nature Communications Here, the authors show that physiological alpha-synuclein supports mitochondrial ATP homeostasis via interactions with ATP synthase and AK2, whereas its disease-linked mutants, truncated forms, and ag...

Excited to play a small role in this great paper: www.nature.com/articles/s41... by providing high quality purified chaperones by@masgu.bsky.social ! Huge congrats to first authors Tetiana Serdiuk and Yanick Fleischmann and the @picottilab.bsky.social and Roland Riek's lab for their work!

A benchmark dataset of 614 experimentally characterized de novo designed monomers from 11 different design studies shows that:
- deep learning structural metrics only weakly predict success
- The score distribution is different for different types of structures

@grocklin.bsky.social

Thrilled our PANCS-binder tech is finally out in print!
www.nature.com/articles/s41...

This technology, 11-years in the making, has transformed how we do research in my lab, and was led by an amazing postdoc, Matt Styles, who is currently entering the academic job market - so look out for him! 1/n

Scaling down protein language modeling with MSA Pairformer Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...

Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

ChimeraX daily builds can predict binding affinity of small molecules using Boltz 2 on your Mac, Windows or Linux computer. www.rbvi.ucsf.edu/chimerax/dat...

when they close it all up, I do believe this will go down as the funniest video on the internet

Global Kinetic-Thermodynamic Responses: Derivation of a General Non-Linear Equation and Demonstrations on Chemical Reactions How to accelerate a reaction has been a critical question in physical organic chemistry, eliciting multiple models describing the interplay between kinetics and thermodynamic driving forces. However, ...

Global Kinetic-Thermodynamic Responses: Derivation of a General Non-Linear Equation and Demonstrations on Chemical Reactions | ChemRxiv - doi.org/10.26434/che... #compchem

Super excited 3 days at the CECAM workshop co-organized with @drgregbowman.bsky.social @bettinagkeller.bsky.social! Protein dynamics is definitely shaping up to be the next big topic in AI for Science! Huge thanks to @cecamevents.bsky.social, @uwdsi.bsky.social, TCI, Chem, Emma and the DSI staff!

This was a great meeting! Kudos to @xuhuihuangchem.bsky.social‬ and UW for being such great hosts. Now to talk with the dean to get lake and brat stand at Temple...

This week @uwdsi.bsky.social is hosting the @cecamevents.bsky.social Flagship Workshop on
Biomolecular Dynamics in the Age of Machine Learning, organized by DSI affiliate @xuhuihuangchem.bsky.social @drgregbowman.bsky.social & Bettina Keller @uwmadisonchem.bsky.social
www.cecam.org/workshop-det...

Partially-latent flow matching enables sequence-structure codesign of large proteins and functional motif scaffolding.

@kdidi.bsky.social @machine.learning.bio @karstenkreis.bsky.social @arashv.bsky.social

arxiv.org/html/2507.09...

I am on a glide path to retirement. So my colleagues are looking for a new physical/analytical chemist. I have had a terrific 40 year run at Bryn Mawr…and will miss the students a ton. #chemsky #womeninSTEM apply.interfolio.com/170426

Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics?

@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!

🧵

BioEmu now published in @science.org !!

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