Pablo Arantes
@pabloarantes.bsky.social
#compchem Research Scientist at Vita Nova Institute- Work interests mostly related to the simulation of biomolecular systems - Lead developer of the Making It Rain, Cloud-Bind and ParametrizANI projects.
https://pablo-arantes.github.io/
https://pablo-arantes.github.io/
Pinned
Pablo Arantes
@pabloarantes.bsky.social
· Aug 20
ParametrizANI: Fast, Accurate, and Free Parametrization for Small Molecules
In molecular studies, the accurate parametrization of small molecules stands as an essential yet growing demand. Addressing this, we introduce ParametrizANI, a tool crafted explicitly for establishing...
doi.org
Exciting news for molecular research! Introducing ParametrizANI: a fast, accurate, & free tool for small molecule parametrization! We're democratizing research, enabling teams of all sizes to perform dihedral parametrization with DFT-level accuracy. 1/8
doi.org/10.26434/che...
doi.org/10.26434/che...
🧠💥 ParametrizANI found a home!
Our paper is now published in JCIM!
Making ML-based force field parametrization open and easy for everyone.
With TorchANI, @rdkit.bsky.social & @openmm.org
🔗 pubs.acs.org/doi/abs/10.1...
@acs.org @giuliapalermo.bsky.social
Our paper is now published in JCIM!
Making ML-based force field parametrization open and easy for everyone.
With TorchANI, @rdkit.bsky.social & @openmm.org
🔗 pubs.acs.org/doi/abs/10.1...
@acs.org @giuliapalermo.bsky.social
October 9, 2025 at 1:02 PM
🧠💥 ParametrizANI found a home!
Our paper is now published in JCIM!
Making ML-based force field parametrization open and easy for everyone.
With TorchANI, @rdkit.bsky.social & @openmm.org
🔗 pubs.acs.org/doi/abs/10.1...
@acs.org @giuliapalermo.bsky.social
Our paper is now published in JCIM!
Making ML-based force field parametrization open and easy for everyone.
With TorchANI, @rdkit.bsky.social & @openmm.org
🔗 pubs.acs.org/doi/abs/10.1...
@acs.org @giuliapalermo.bsky.social
Your protein moves, but when exactly? ⏱️
Meet eRMSF, our new Python tool that tracks fluctuations over time!
Traditional RMSF shows “how much.”
eRMSF shows “when.” 🔥
Preprint 🔗 doi.org/10.26434/che...
GitHub github.com/pablo-arante...
Try it on Colab → colab.research.google.com/github/pablo...
Meet eRMSF, our new Python tool that tracks fluctuations over time!
Traditional RMSF shows “how much.”
eRMSF shows “when.” 🔥
Preprint 🔗 doi.org/10.26434/che...
GitHub github.com/pablo-arante...
Try it on Colab → colab.research.google.com/github/pablo...
October 7, 2025 at 1:12 PM
Your protein moves, but when exactly? ⏱️
Meet eRMSF, our new Python tool that tracks fluctuations over time!
Traditional RMSF shows “how much.”
eRMSF shows “when.” 🔥
Preprint 🔗 doi.org/10.26434/che...
GitHub github.com/pablo-arante...
Try it on Colab → colab.research.google.com/github/pablo...
Meet eRMSF, our new Python tool that tracks fluctuations over time!
Traditional RMSF shows “how much.”
eRMSF shows “when.” 🔥
Preprint 🔗 doi.org/10.26434/che...
GitHub github.com/pablo-arante...
Try it on Colab → colab.research.google.com/github/pablo...
Reposted by Pablo Arantes
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 Pablo Arantes
When Pablo told me about this idea, I could see an immediate impact on drug discovery endeavors.
People can easily refine parameters of multiple dihedral torsion for hundreds of molecules and employ those in FEP simulations.
10/10 recommend 👍
People can easily refine parameters of multiple dihedral torsion for hundreds of molecules and employ those in FEP simulations.
10/10 recommend 👍
Exciting news for molecular research! Introducing ParametrizANI: a fast, accurate, & free tool for small molecule parametrization! We're democratizing research, enabling teams of all sizes to perform dihedral parametrization with DFT-level accuracy. 1/8
doi.org/10.26434/che...
doi.org/10.26434/che...
ParametrizANI: Fast, Accurate, and Free Parametrization for Small Molecules
In molecular studies, the accurate parametrization of small molecules stands as an essential yet growing demand. Addressing this, we introduce ParametrizANI, a tool crafted explicitly for establishing...
doi.org
August 20, 2025 at 6:43 PM
When Pablo told me about this idea, I could see an immediate impact on drug discovery endeavors.
People can easily refine parameters of multiple dihedral torsion for hundreds of molecules and employ those in FEP simulations.
10/10 recommend 👍
People can easily refine parameters of multiple dihedral torsion for hundreds of molecules and employ those in FEP simulations.
10/10 recommend 👍
Reposted by Pablo Arantes
New from our lab!
🚀 ParametrizANI - a #NeuralNetworks tool for molecular parametrization.
Predicts potential energy surfaces with near-DFT/CC accuracy, at a fraction of the computational cost!
#AI #QuantumChemistry #CompChem #ML 🤖
chemrxiv.org/engage/chemr...
Try it:
github.com/palermolab/P...
🚀 ParametrizANI - a #NeuralNetworks tool for molecular parametrization.
Predicts potential energy surfaces with near-DFT/CC accuracy, at a fraction of the computational cost!
#AI #QuantumChemistry #CompChem #ML 🤖
chemrxiv.org/engage/chemr...
Try it:
github.com/palermolab/P...
GitHub - palermolab/ParametrizANI: ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI
ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI - palermolab/ParametrizANI
github.com
August 20, 2025 at 5:33 PM
New from our lab!
🚀 ParametrizANI - a #NeuralNetworks tool for molecular parametrization.
Predicts potential energy surfaces with near-DFT/CC accuracy, at a fraction of the computational cost!
#AI #QuantumChemistry #CompChem #ML 🤖
chemrxiv.org/engage/chemr...
Try it:
github.com/palermolab/P...
🚀 ParametrizANI - a #NeuralNetworks tool for molecular parametrization.
Predicts potential energy surfaces with near-DFT/CC accuracy, at a fraction of the computational cost!
#AI #QuantumChemistry #CompChem #ML 🤖
chemrxiv.org/engage/chemr...
Try it:
github.com/palermolab/P...
Exciting news for molecular research! Introducing ParametrizANI: a fast, accurate, & free tool for small molecule parametrization! We're democratizing research, enabling teams of all sizes to perform dihedral parametrization with DFT-level accuracy. 1/8
doi.org/10.26434/che...
doi.org/10.26434/che...
ParametrizANI: Fast, Accurate, and Free Parametrization for Small Molecules
In molecular studies, the accurate parametrization of small molecules stands as an essential yet growing demand. Addressing this, we introduce ParametrizANI, a tool crafted explicitly for establishing...
doi.org
August 20, 2025 at 1:34 PM
Exciting news for molecular research! Introducing ParametrizANI: a fast, accurate, & free tool for small molecule parametrization! We're democratizing research, enabling teams of all sizes to perform dihedral parametrization with DFT-level accuracy. 1/8
doi.org/10.26434/che...
doi.org/10.26434/che...
Reposted by Pablo Arantes
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...
github.com/martinpacesa...
June 30, 2025 at 7:45 PM
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...
github.com/martinpacesa...
Reposted by Pablo Arantes
🚨BREAKING: 300+ NIH employees call out the harm of censorship & politicized science in scathing email to Bhattacharya, demanding an end to political interference, a lift on funding freezes, & rehiring of fired staff whose work saves lives.
This is historic - insiders are blowing the whistle.
🧵(1/5)
This is historic - insiders are blowing the whistle.
🧵(1/5)
June 9, 2025 at 12:03 PM
🚨BREAKING: 300+ NIH employees call out the harm of censorship & politicized science in scathing email to Bhattacharya, demanding an end to political interference, a lift on funding freezes, & rehiring of fired staff whose work saves lives.
This is historic - insiders are blowing the whistle.
🧵(1/5)
This is historic - insiders are blowing the whistle.
🧵(1/5)
Reposted by Pablo Arantes
🚀 Excited to release BoltzDesign1!
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
June 3, 2025 at 1:31 AM
🚀 Excited to release BoltzDesign1!
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
This is the kind of message that makes it all worth it.
When someone takes a moment to say thank you, it reminds me why we keep pushing forward—sharing tools, writing posts, and trying to make science more open and accessible. Grateful for the kind words!
When someone takes a moment to say thank you, it reminds me why we keep pushing forward—sharing tools, writing posts, and trying to make science more open and accessible. Grateful for the kind words!
April 8, 2025 at 10:25 PM
This is the kind of message that makes it all worth it.
When someone takes a moment to say thank you, it reminds me why we keep pushing forward—sharing tools, writing posts, and trying to make science more open and accessible. Grateful for the kind words!
When someone takes a moment to say thank you, it reminds me why we keep pushing forward—sharing tools, writing posts, and trying to make science more open and accessible. Grateful for the kind words!
Our latest paper just dropped in PNAS! 🎉
Turns out, CRISPR-associated transposons don’t just jump—they dance their way through DNA! 🕺🔬
Exciting times for genome engineering!
🧬 Read more in PNAS: www.pnas.org/doi/10.1073/...
#CRISPR #GeneEditing #PNAS #MDsimulations #CompChem
Turns out, CRISPR-associated transposons don’t just jump—they dance their way through DNA! 🕺🔬
Exciting times for genome engineering!
🧬 Read more in PNAS: www.pnas.org/doi/10.1073/...
#CRISPR #GeneEditing #PNAS #MDsimulations #CompChem
April 2, 2025 at 7:12 PM
Our latest paper just dropped in PNAS! 🎉
Turns out, CRISPR-associated transposons don’t just jump—they dance their way through DNA! 🕺🔬
Exciting times for genome engineering!
🧬 Read more in PNAS: www.pnas.org/doi/10.1073/...
#CRISPR #GeneEditing #PNAS #MDsimulations #CompChem
Turns out, CRISPR-associated transposons don’t just jump—they dance their way through DNA! 🕺🔬
Exciting times for genome engineering!
🧬 Read more in PNAS: www.pnas.org/doi/10.1073/...
#CRISPR #GeneEditing #PNAS #MDsimulations #CompChem
I have included side-chain reconstruction using HPacker in the BioEmu Notebook. Thank you to @martinsteinegger.bsky.social whose notebook provided inspiration for incorporating the cell to add side-chain reconstruction.
🔗 Try it on Google Colab: colab.research.google.com/github/pablo...
🔗 Try it on Google Colab: colab.research.google.com/github/pablo...
I’ve just updated the BioEmu notebook to include the powerful LogMD. Now, you can generate equilibrium ensembles and explore the full ensemble directly in the notebook.
A huge thanks to Alexander Mathiasen for the support! 🙌
🔗 Try it on Google Colab: lnkd.in/gcuqd-fT
A huge thanks to Alexander Mathiasen for the support! 🙌
🔗 Try it on Google Colab: lnkd.in/gcuqd-fT
April 2, 2025 at 12:34 AM
I have included side-chain reconstruction using HPacker in the BioEmu Notebook. Thank you to @martinsteinegger.bsky.social whose notebook provided inspiration for incorporating the cell to add side-chain reconstruction.
🔗 Try it on Google Colab: colab.research.google.com/github/pablo...
🔗 Try it on Google Colab: colab.research.google.com/github/pablo...
I’ve just updated the BioEmu notebook to include the powerful LogMD. Now, you can generate equilibrium ensembles and explore the full ensemble directly in the notebook.
A huge thanks to Alexander Mathiasen for the support! 🙌
🔗 Try it on Google Colab: lnkd.in/gcuqd-fT
A huge thanks to Alexander Mathiasen for the support! 🙌
🔗 Try it on Google Colab: lnkd.in/gcuqd-fT
March 20, 2025 at 6:09 PM
I’ve just updated the BioEmu notebook to include the powerful LogMD. Now, you can generate equilibrium ensembles and explore the full ensemble directly in the notebook.
A huge thanks to Alexander Mathiasen for the support! 🙌
🔗 Try it on Google Colab: lnkd.in/gcuqd-fT
A huge thanks to Alexander Mathiasen for the support! 🙌
🔗 Try it on Google Colab: lnkd.in/gcuqd-fT
🚀 Making it Rain ☁️💦 just got an AI-powered upgrade! 🚀
First, we made MD simulations rain down from the cloud. Now, we’re bringing deep learning into the mix! 🌩️🤖
First, we made MD simulations rain down from the cloud. Now, we’re bringing deep learning into the mix! 🌩️🤖
a robot says hey guys in a purple light
ALT: a robot says hey guys in a purple light
media.tenor.com
March 1, 2025 at 1:36 AM
🚀 Making it Rain ☁️💦 just got an AI-powered upgrade! 🚀
First, we made MD simulations rain down from the cloud. Now, we’re bringing deep learning into the mix! 🌩️🤖
First, we made MD simulations rain down from the cloud. Now, we’re bringing deep learning into the mix! 🌩️🤖
Just a small lesson for our dear American friends…😉
Breaking News: Jair Bolsonaro, Brazil’s former president, was charged with overseeing a vast scheme to overturn the 2022 election he lost.
Brazil Charges Bolsonaro With Attempting a Coup
Brazil’s attorney general charged the former president Jair Bolsonaro with trying to overturn the 2022 elections.
www.nytimes.com
February 19, 2025 at 12:44 AM
Just a small lesson for our dear American friends…😉
Reposted by Pablo Arantes
How completely jealous am I of Brazil right now
Brazil Charges Bolsonaro With Attempting a Coup (Gift Article)
Brazil’s attorney general charged the former president Jair Bolsonaro with trying to overturn the 2022 elections.
www.nytimes.com
February 19, 2025 at 12:34 AM
How completely jealous am I of Brazil right now
Reposted by Pablo Arantes
🚀 First Bluesky Post! 🎉 VMD 2.0 Alpha is here! Released today at BPS 2025, this is the biggest update in 30 years—new UI, real-time ray tracing, fast surfaces, UHD & touchscreen support. Monthly updates coming in 2025! Try it now! #VMD #BPS2025 #MolecularVisualization
www.ks.uiuc.edu/Research/vmd...
www.ks.uiuc.edu/Research/vmd...
February 17, 2025 at 6:56 AM
🚀 First Bluesky Post! 🎉 VMD 2.0 Alpha is here! Released today at BPS 2025, this is the biggest update in 30 years—new UI, real-time ray tracing, fast surfaces, UHD & touchscreen support. Monthly updates coming in 2025! Try it now! #VMD #BPS2025 #MolecularVisualization
www.ks.uiuc.edu/Research/vmd...
www.ks.uiuc.edu/Research/vmd...
Reposted by Pablo Arantes
The d0 is key to eliminating the dependence of the TM score on alignment/structure length. It's easier for two short proteins to be randomly similar than it is for two very large proteins. A bit Bayesian: short proteins require better evidence for similarity than large ones. Better p(data | model)
February 16, 2025 at 2:13 AM
The d0 is key to eliminating the dependence of the TM score on alignment/structure length. It's easier for two short proteins to be randomly similar than it is for two very large proteins. A bit Bayesian: short proteins require better evidence for similarity than large ones. Better p(data | model)
Reposted by Pablo Arantes
Molecular dynamics requires a lot of expert knowledge to set-up and analyze simulations. We set out to automate it with LLM agents: MDCrow!
February 14, 2025 at 11:05 PM
Molecular dynamics requires a lot of expert knowledge to set-up and analyze simulations. We set out to automate it with LLM agents: MDCrow!
Reposted by Pablo Arantes
Do you want to know why #ABE 8e is the most efficient adenine base editor? Read our paper with the amazing
Audrey Lapinaite!
@narjournal.bsky.social
The dimerization of TadA8e and its exclusive interactions with #CRISPR Cas9 boost #BaseEditing efficiency!
academic.oup.com/nar/article/...
Audrey Lapinaite!
@narjournal.bsky.social
The dimerization of TadA8e and its exclusive interactions with #CRISPR Cas9 boost #BaseEditing efficiency!
academic.oup.com/nar/article/...
Dimerization of the deaminase domain and locking interactions with Cas9 boost base editing efficiency in ABE8e
Abstract. CRISPR-based DNA adenine base editors (ABEs) hold remarkable promises to address human genetic diseases caused by point mutations. ABEs were deve
academic.oup.com
February 8, 2025 at 6:17 PM
Do you want to know why #ABE 8e is the most efficient adenine base editor? Read our paper with the amazing
Audrey Lapinaite!
@narjournal.bsky.social
The dimerization of TadA8e and its exclusive interactions with #CRISPR Cas9 boost #BaseEditing efficiency!
academic.oup.com/nar/article/...
Audrey Lapinaite!
@narjournal.bsky.social
The dimerization of TadA8e and its exclusive interactions with #CRISPR Cas9 boost #BaseEditing efficiency!
academic.oup.com/nar/article/...
Reposted by Pablo Arantes
Bom dia!
“Tú no puedes comprar al viento
Tú no puedes comprar al sol
Tú no puedes comprar la lluvia
Tú no puedes comprar el calor”
“Tú no puedes comprar al viento
Tú no puedes comprar al sol
Tú no puedes comprar la lluvia
Tú no puedes comprar el calor”
January 27, 2025 at 11:09 AM
Bom dia!
“Tú no puedes comprar al viento
Tú no puedes comprar al sol
Tú no puedes comprar la lluvia
Tú no puedes comprar el calor”
“Tú no puedes comprar al viento
Tú no puedes comprar al sol
Tú no puedes comprar la lluvia
Tú no puedes comprar el calor”
Reposted by Pablo Arantes
Have any academic researchers started hearing about cuts/holds on federal grants from other federal agencies outside of NIH? I got a concerning message today about a grant hold, and it seems to be the same politics. Not surprising, but further worrying ... 😨
January 23, 2025 at 5:09 PM
Have any academic researchers started hearing about cuts/holds on federal grants from other federal agencies outside of NIH? I got a concerning message today about a grant hold, and it seems to be the same politics. Not surprising, but further worrying ... 😨
Reposted by Pablo Arantes
Nazis: "that's a nazi salute"
Historians: "that's a nazi salute"
Average person: "that's a nazi salute"
The Media: "Elon Musk makes odd gesture throwing his heart to the crowd."
Historians: "that's a nazi salute"
Average person: "that's a nazi salute"
The Media: "Elon Musk makes odd gesture throwing his heart to the crowd."
January 21, 2025 at 1:03 AM
Nazis: "that's a nazi salute"
Historians: "that's a nazi salute"
Average person: "that's a nazi salute"
The Media: "Elon Musk makes odd gesture throwing his heart to the crowd."
Historians: "that's a nazi salute"
Average person: "that's a nazi salute"
The Media: "Elon Musk makes odd gesture throwing his heart to the crowd."
It’s Nazi gestures, Nazi aesthetics, Nazi rhetoric, Nazi symbols. But they’re not Nazis, okay?
January 21, 2025 at 2:19 AM
It’s Nazi gestures, Nazi aesthetics, Nazi rhetoric, Nazi symbols. But they’re not Nazis, okay?
Reposted by Pablo Arantes
So seems like the group is on a roll this month!
Here’s our latest work on parametrising coarse-grained models of sugars (disaccharides) by Astrid Brandner & in collaboration with Iain Smith, @pauloctsouza.bsky.social and @cg-martini.bsky.social pubs.acs.org/doi/10.1021/... #glycotime
Here’s our latest work on parametrising coarse-grained models of sugars (disaccharides) by Astrid Brandner & in collaboration with Iain Smith, @pauloctsouza.bsky.social and @cg-martini.bsky.social pubs.acs.org/doi/10.1021/... #glycotime
Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field
Sugars are ubiquitous in biology; they occur in all kingdoms of life. Despite their prevalence, they have often been somewhat neglected in studies of structure–dynamics–function relationships of macro...
pubs.acs.org
January 17, 2025 at 12:27 PM
So seems like the group is on a roll this month!
Here’s our latest work on parametrising coarse-grained models of sugars (disaccharides) by Astrid Brandner & in collaboration with Iain Smith, @pauloctsouza.bsky.social and @cg-martini.bsky.social pubs.acs.org/doi/10.1021/... #glycotime
Here’s our latest work on parametrising coarse-grained models of sugars (disaccharides) by Astrid Brandner & in collaboration with Iain Smith, @pauloctsouza.bsky.social and @cg-martini.bsky.social pubs.acs.org/doi/10.1021/... #glycotime