Vincent Voelz
@voelzlab.bsky.social
Professor of Chemistry at Temple University. Molecular simulation, stat mech, ML/DL, protein dynamics, biophysics, Bayesian inference, computational design, drug discovery.
https://orcid.org/0000-0002-1054-2124
https://sites.temple.edu/voelzlab
https://orcid.org/0000-0002-1054-2124
https://sites.temple.edu/voelzlab
Reposted by 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...
Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0]
| Living Journal of Computational Molecular Science
doi.org
October 28, 2025 at 5:59 PM
Excited to be a part of this review paper by Chapin Cavender et al. Now out in LiveCoMS! doi.org/10.33011/liv...
Reposted by Vincent Voelz
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
Learn more here: buff.ly/gInH6VV
#SBGrid #SBGridSoftware #StructuralBiology
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…
buff.ly
October 24, 2025 at 4:08 PM
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
Learn more here: buff.ly/gInH6VV
#SBGrid #SBGridSoftware #StructuralBiology
Reposted by Vincent Voelz
📢 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. 🧵👇
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. 🧵👇
October 18, 2025 at 6:59 PM
📢 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. 🧵👇
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. 🧵👇
Reposted by Vincent Voelz
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...
Check out this new interview with Pat in Nature Reviews Drug Discovery:
www.nature.com/articles/d41...
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.
www.nature.com
October 15, 2025 at 3:23 PM
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...
Check out this new interview with Pat in Nature Reviews Drug Discovery:
www.nature.com/articles/d41...
Reposted by Vincent Voelz
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 👇)
October 15, 2025 at 12:22 PM
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 👇)
Reposted by Vincent Voelz
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 15, 2025 at 5:19 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Vincent Voelz
Out in its final form
pubs.acs.org/doi/10.1021/...
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
September 17, 2025 at 9:02 AM
Out in its final form
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Reposted by Vincent Voelz
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...
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
September 16, 2025 at 7:21 PM
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...
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...
Reposted by Vincent Voelz
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]
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]
May 23, 2025 at 4:13 PM
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]
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]
Reposted by Vincent Voelz
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...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
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...
www.nature.com/articles/s41...
Reposted by Vincent Voelz
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
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
August 19, 2025 at 7:42 AM
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
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
Reposted by Vincent Voelz
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....
🔗 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
August 19, 2025 at 3:57 PM
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....
🔗 doi.org/10.1021/acs....
Reposted by Vincent Voelz
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...
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
August 18, 2025 at 8:26 PM
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...
The winners are being acknowledged for their outstanding achievements in chemistry across various fields in the discipline. cen.acs.org/people/award...
Reposted by Vincent Voelz
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
bit.ly/4lnVYOs
August 12, 2025 at 7:07 PM
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
bit.ly/4lnVYOs
Reposted by Vincent Voelz
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...
Link: www.nature.com/articles/s41...
August 18, 2025 at 5:46 PM
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...
Link: www.nature.com/articles/s41...
Reposted by Vincent Voelz
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
August 18, 2025 at 2:11 PM
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!
Reposted by Vincent Voelz
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
- deep learning structural metrics only weakly predict success
- The score distribution is different for different types of structures
@grocklin.bsky.social
August 8, 2025 at 8:10 PM
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
- deep learning structural metrics only weakly predict success
- The score distribution is different for different types of structures
@grocklin.bsky.social
Reposted by Vincent Voelz
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
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
August 6, 2025 at 5:54 PM
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
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
Reposted by Vincent Voelz
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🧵
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
August 5, 2025 at 6:31 AM
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🧵
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🧵
Reposted by Vincent Voelz
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...
July 24, 2025 at 2:44 AM
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...
Reposted by Vincent Voelz
when they close it all up, I do believe this will go down as the funniest video on the internet
July 24, 2025 at 7:51 PM
when they close it all up, I do believe this will go down as the funniest video on the internet
Reposted by Vincent Voelz
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
July 21, 2025 at 8:48 AM
Global Kinetic-Thermodynamic Responses: Derivation of a General Non-Linear Equation and Demonstrations on Chemical Reactions | ChemRxiv - doi.org/10.26434/che... #compchem
Reposted by Vincent Voelz
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!
July 19, 2025 at 5:05 PM
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!