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/
🧠💥 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...
Our user-friendly Jupyter notebooks provide a complete workflow for dihedral parametrization, from SMILES strings to optimized force field parameters. We support both GAFF & @openforcefield.org force fields, ensuring compatibility for your simulations. #ForceFields 5/8
August 20, 2025 at 1:34 PM
Our user-friendly Jupyter notebooks provide a complete workflow for dihedral parametrization, from SMILES strings to optimized force field parameters. We support both GAFF & @openforcefield.org force fields, ensuring compatibility for your simulations. #ForceFields 5/8
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!
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
Meet BioEmu, a generative AI model for scalable emulation of protein equilibrium ensembles—predicting structural distributions from just an amino acid sequence!
Developed by Microsoft Research & Freie Universität Berlin, this model is reshaping biomolecular modeling.
Picture from BioEmu repository.
Developed by Microsoft Research & Freie Universität Berlin, this model is reshaping biomolecular modeling.
Picture from BioEmu repository.
March 1, 2025 at 1:36 AM
Meet BioEmu, a generative AI model for scalable emulation of protein equilibrium ensembles—predicting structural distributions from just an amino acid sequence!
Developed by Microsoft Research & Freie Universität Berlin, this model is reshaping biomolecular modeling.
Picture from BioEmu repository.
Developed by Microsoft Research & Freie Universität Berlin, this model is reshaping biomolecular modeling.
Picture from BioEmu repository.
ABE8e: the Beyoncé of base editing—flawless dimerization, exclusive interactions, and unparalleled efficiency! 🎤
Check out our latest work: doi.org/10.1093/nar/...
#CRISPR #BaseEditing #ChemComp #MDsimulations
Check out our latest work: doi.org/10.1093/nar/...
#CRISPR #BaseEditing #ChemComp #MDsimulations
November 22, 2024 at 12:20 PM
ABE8e: the Beyoncé of base editing—flawless dimerization, exclusive interactions, and unparalleled efficiency! 🎤
Check out our latest work: doi.org/10.1093/nar/...
#CRISPR #BaseEditing #ChemComp #MDsimulations
Check out our latest work: doi.org/10.1093/nar/...
#CRISPR #BaseEditing #ChemComp #MDsimulations
Just hit 1,000 citations on Google Scholar! That’s one small step for science, one giant leap for my imposter syndrome. 🚀📚😜
November 19, 2024 at 4:22 PM
Just hit 1,000 citations on Google Scholar! That’s one small step for science, one giant leap for my imposter syndrome. 🚀📚😜
Bluesky now has over 10 million users, and I was #678,389!
September 21, 2024 at 1:31 PM
Bluesky now has over 10 million users, and I was #678,389!