Vincent Voelz

something to digest... ;-)

Our recent preprint shows that metastable, short-lived PPIs captured by MD and IGME define key design targets for PROTACs, enabling rational discovery of sub-nanomolar RIPK1 degraders.

Great collab w/ Weiping Tang! Congrats to Yue & co-authors!

chemrxiv.org/doi/full/10....
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Robust and Automated Force Field Parameterization Using Validation Sets and Active Learning Molecular mechanics force fields enable atomistic simulations of complex systems that are too large for a quantum mechanical treatment. Simulation accuracy depends on the parameters employed in the fo...

"In contrast to previous attempts at iterative optimization, we employ a validation set to determine convergence. Using a validation set circumvents problems with parameter convergence and flags when overfitting occurs"

pubs.acs.org/doi/full/10....

New Preprint!! We show that binding entropy can be quantitatively predicted from crystallographic ensemble models, accounting for both protein conformational entropy and solvent entropy! www.biorxiv.org/content/10.6...

Third preprint of the year is from @julianstreit.bsky.social who, with our collaborators at Peptone, show that multithermal On-the-fly Probability Enhanced Sampling (OPES) enables efficient generation of atomistic ensembles for disordered peptides and proteins 🍝

www.biorxiv.org/content/10.6...

The work by @danialv.bsky.social is now out in @pnas.org with a few changes after peer-review. Have a look if you are interested in lipid transport by bridge lipid transfer proteins (BLTPs)...
www.pnas.org/doi/10.1073/...

Congrats Roland!

Quantum quacks Nature Chemistry - It is 100 years since the initial development of quantum mechanics, and not only did it bring with it a greater understanding of the world around us, it also introduced a new...

When I wrote my latest for @natchem.nature.com on the appropriation of the quantum mechanical lexicon by scam artists, could I have imagined that the surgeon general of Florida would be peddling the woo? Alas, probably. rdcu.be/eXQL (1/3)

LAMMPS-ANI: Large Scale Molecular Dynamics Simulations with ANI Neural Network Potential Machine Learning Interatomic Potentials (MLIPs), trained with Quantum Mechanics data, can model potential energy surfaces for molecular systems with very high accuracy and extreme speedups compared to...

New Preprint dropped. LAMMPS + ANI, a super fast implementation of MLIPs. Highly parallel (> 1000 GPUS) and much faster than anything else out there ! Work done by the amazing @ignaciopickering.bsky.social, @nickterrel.bsky.social , and Jinze (Richard) Xue. chemrxiv.org/engage/chemr...

Senior Machine Learning Researcher - MSR AI for Science | Microsoft Careers Invent novel deep learning techniques for models of (bio)molecular structure, dynamics, reactivity and function. Design, implement, and iterate on model architectures and training algorithms (e.g., di...

#MachineLearning researchers: Join us at @msftresearch.bsky.social #ArtificialIntelligence for Science to push the frontier of AI for molecular Biology or AI for Chemistry. Work with @marwinsegler.bsky.social or my team in Berlin, Cambridge or Amsterdam.

apply.careers.microsoft.com/careers/job/...

How do cells know which way to move in a chemical gradient? 🧭 New work by graduate student Andrew Goetz proposes that receptors can compute direction. This new mechanism for directional sensing was published in PNAS late last year: www.pnas.org/doi/10.1073/...

Exciting news! We have a new website: omsf.io/alchemistry

Your one-stop shop for everything related to our conference community. 🎉

BTW, registration is now open, so head over to secure your spot! We'll be sharing updates and details about the event.

Bookmark it as there's plenty more to come!

Insights into the Electronic and Structural Properties of Cellulose and Amylose: A Comparative Force Field Study Amylose and cellulose are important biopolymers with diverse applications in biotechnology and materials science. Understanding their structural, dynamic, and solvation properties at the molecular level is critical for harnessing their potential. This study investigates the electronic and structural properties of single-chain cellulose and single- and double-chain amylose in aqueous solution using molecular dynamics simulations with both nonpolarizable (CHARMM) and polarizable (Drude) force fields. CHARMM simulations show stable hydrogen bonding between amylose and water, higher glucose ring dipole moments, increased rigidity, adoption of chair conformations, and less variation in dihedral angles. In contrast, Drude simulations captured dynamic electronic polarization, enhanced conformational flexibility, and resulted in heterogeneous inter- and intramolecular hydrogen bonds. For cellulose, structural and solvation behaviors were largely similar between CHARMM and Drude. These findings highlight molecular interactions and solvation dynamics of amylose and cellulose, with potential relevance in materials science and biotechnology.

First article of 2026! Happy to have our first real foray into carbohydrates out in J Phys Chem B. Excellent work by PhD candidate Esmat Mohammadi.

pubs.acs.org/doi/full/10....

Large-scale collaborative assessment of binding free energy calculations for drug discovery using OpenFE Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav...

OpenFE is ready for production! chemrxiv.org/engage/chemr...

In collaboration with our industry partners, we ran benchmarking simulations of our hybrid-topology RBFE protocol on a large collection of both public and private protein-ligand binding datasets.

#compchem

AlphaFold is five years old — these charts show how it revolutionized science Since it was unveiled in 2020, Google DeepMind's game-changing AI tool has helped researchers all over the world to predict the 3D structures of hundreds of millions of proteins.

www.nature.com/articles/d41...

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/...

Screen binders using ipSAE YouTube video by ProteinDesignStudio

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