Pablo Arantes
#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.
pablo-arantes.github.io
- Reposted by Pablo ArantesI'm super excited to announce the first preprint of my PhD, together with Chenxi Ou and @sokrypton.org! ML has revolutionized protein modeling, but crucial challenges remain. For example, we can't reliably predict complicated protein structures without MSAs, which limits what we can design.
- 🎉 New publication in JCIM at @pubs.acs.org! We present eRMSF, a Python package for ensemble-based RMSF analysis of biomolecular systems, supporting MD, PDB, and ML ensembles. Proud to collaborate with Rodrigo Ligabue-Braun and @conradopedebos.bsky.social pubs.acs.org/doi/10.1021/...
- 🧠💥 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
- 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...
- Reposted by Pablo ArantesExciting 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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- Reposted by Pablo ArantesNew 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...
- 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...
- How? ParametrizANI uses the robust PyTorch-based TorchANI program & ANI deep learning models (ANI-1x, ANI-2x). This predicts potential energy surfaces with near-DFT or coupled-cluster accuracy, at a fraction of the computational cost! #DeepLearning #TorchANI #AIforScience 2/8
- Reposted by Pablo ArantesWe 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...
- 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)
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- 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!
- 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
- New paper from our lab just out @pnas.org! 🚀 Using free energy simulations, #AIphaFold and #cryoEM refinement, we uncovered a key conformational change in a paradigm-shifting #CRISPR-associated #transposon capable of precise gene knock-ins. 🔍🧬 www.pnas.org/doi/epub/10....
- 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...
- 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
- 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
- 🎓 BioEmu is based on the paper: 📄 Scalable emulation of protein equilibrium ensembles with generative deep learning 👨🔬 Authors: SarahLewis & @franknoe.bsky.social (corresponding), et al. 📌 Read it here: doi.org/10.1101/2024...
- 🚀 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! 🌩️🤖
- Just a small lesson for our dear American friends…😉
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- 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...
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- Reposted by Pablo ArantesMolecular dynamics requires a lot of expert knowledge to set-up and analyze simulations. We set out to automate it with LLM agents: MDCrow!
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- Reposted by Pablo ArantesNazis: "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."
- It’s Nazi gestures, Nazi aesthetics, Nazi rhetoric, Nazi symbols. But they’re not Nazis, okay?
- Reposted by Pablo ArantesSo 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
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- New season of The Handmaid's Tale starts on Monday, 20 January 2025.
- Nailed it! 🎯
- Reposted by Pablo ArantesSuper excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...
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- Reposted by Pablo Arantesgo.bsky.app/Qc4frbt Made a starter pack for computational chemists, let me know who I missed please @jchodera.bsky.social @olexandr.bsky.social @jelfschem.bsky.socialat://did:plc:no3avbdkex2mxmt4ulea5jyj/app.bsky.graph.starterpack/3laqzdsxhds2a
- 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
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- Just hit 1,000 citations on Google Scholar! That’s one small step for science, one giant leap for my imposter syndrome. 🚀📚😜
- Reposted by Pablo Arantes🚨Announcing NetSci: a super fast tool to compute correlated motion in biomolecules pubs.acs.org/doi/10.1021/... @pabloarantes.bsky.social & team also made it into a Colab notebook: colab.research.google.com/drive/1GGJKr... Give it a try & send feedback!
- Accessing GPU clusters or high-performance computers can be a challenge in Brazil, so I created a Colab notebook for NetSci to perform GC analysis. It works seamlessly, even with Colab’s free tier! Check it out here: colab.research.google.com/drive/1GGJKr... Paper: t.co/evNxaX2omW
- Bluesky now has over 10 million users, and I was #678,389!
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- Reposted by Pablo Aranteswow... welcome to the ONE MILLION new users in the last three days!!! 🎉 uau... bem-vindos ao UM MILHÃO de novos usuários nos últimos três dias!!! 🎉
