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Reposted by Vincent Voelz

David De Sancho @daviddesancho.bsky.social · 25d

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

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...

pubs.acs.org

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Reposted by Vincent Voelz

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 26d

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...

Screen binders using ipSAE

YouTube video by ProteinDesignStudio

www.youtube.com

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Reposted by Vincent Voelz

The Matter Lab @thematterlab.bsky.social · May 23

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]

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Reposted by Vincent Voelz

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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Reinier de Vries @reinierdevries.bsky.social · Aug 19

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

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Reposted by Vincent Voelz

Dylan N. (They/Them) @kpmanstheorem.bsky.social · Aug 19

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....

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...

doi.org

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C&EN (Chemical & Engineering News) @cenmag.bsky.social · Aug 18

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...

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

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Reposted by Vincent Voelz

Matthieu Schapira @mattschap.bsky.social · Aug 12

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

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The Matter Lab @thematterlab.bsky.social · Aug 18

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...

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Reposted by Vincent Voelz

HillerLab @hillerlab.bsky.social · Aug 18

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

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...

www.nature.com

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Reposted by Vincent Voelz

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Aug 8

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

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Reposted by Vincent Voelz

Bryan Dickinson @chembiobryan.bsky.social · Aug 6

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

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Yo Akiyama @yoakiyama.bsky.social · Aug 5

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🧵

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 ...

biorxiv.org

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Reposted by Vincent Voelz

ChimeraX @chimerax.ucsf.edu · Jul 24

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...

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Reposted by Vincent Voelz

Tim Onion @bencollins.bsky.social · Jul 24

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

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Reposted by Vincent Voelz

Jan H. Jensen @janhjensen.bsky.social · Jul 21

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

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, ...

doi.org

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Reposted by Vincent Voelz

Xuhui Huang @xuhuihuangchem.bsky.social · Jul 19

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!

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Vincent Voelz @voelzlab.bsky.social · Jul 18

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...

Xuhui Huang @xuhuihuangchem.bsky.social · Jul 14

Squeaks, brats, and Spotted Cows! Warmed up for the CECAM Flagship Workshop “Biomolecular Dynamics in the Age of Machine Learning” starting tomorrow — the first CECAM workshop in Wisconsin! @bettinagkeller.bsky.social @drgregbowman.bsky.social @cecamevents.bsky.social

www.cecam.org/workshop-det...

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Kyle Cranmer @kylecranmer.bsky.social · Jul 15

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...

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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Jul 16

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...

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Michelle Francl @michellefrancl.bsky.social · Jul 16

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

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

apply.interfolio.com

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Gina El Nesr @ginaelnesr.bsky.social · Mar 20

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!

🧵

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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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MDAnalysis @mdanalysis.bsky.social · Jul 11

🚨 Deadline coming up!
🎯 Don’t miss your chance to present at the #mdaUGM2025 — abstract + travel bursary applications due July 15!

Meet the community, share your work, learn from others, and get support to attend.

🔗 Info: www.mdanalysis.org/pages/ugm2025/

#MDAnalysis #OSS #MolecularDynamics #UGM

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Reposted by Vincent Voelz

Frank Noe @franknoe.bsky.social · Jul 11

@maxhenrybarnhart.bsky.social has written a really nice piece on BioEmu for Chemical & Engineering news.

cen.acs.org/biological-c...

Microsoft AI predicts protein conformations

The open-source tool goes beyond AlphaFold by finding proteins’ multiple equilibrium states and free energies

cen.acs.org

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