🚀 ParametrizANI is now a Python package! From SMILES to AMBER/GROMACS/OpenMM force field parameters in one script, powered by neural network potentials (TorchANI, MACE-OFF, AIMNet2, xTB). DFT-level accuracy, CPU-only. 📦 github.com/pablo-arantes/ParametrizANI 📚 parametrizani.readthedocs.io 🧵1/4

GitHub - pablo-arantes/ParametrizANI: Free Parametrization for Small Molecules

Free Parametrization for Small Molecules. Contribute to pablo-arantes/ParametrizANI development by creating an account on GitHub.

github.com

I'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/...

eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems

Understanding molecular flexibility and dynamics across different structural ensembles is essential for interpreting the behavior of complex biological systems. Here, we introduce eRMSF, a fast and user-friendly Python package built with MDAKit from MDAnalysis, designed to perform ensemble-based root mean square fluctuation (RMSF) analyses. Unlike traditional approaches limited to molecular dynamics trajectories, eRMSF extends flexibility analysis to ensembles generated by different methods, such as MD simulations, BioEmu (a deep learning tool for equilibrium ensemble prediction), subsampled AlphaFold2 (AlphaFold ensemble generation), and other computational or experimental sources. By enabling RMSF calculations across heterogeneous ensembles, eRMSF provides a unified framework to evaluate residue or atomic fluctuations in both simulated and predicted structures. Users can easily customize atom, residue, or region selections, tailoring analyses to specific research questions. This approach delivers high-resolution insights into localized motions, complements global stability assessments, and reveals dynamic regions often overlooked by single-method analyses. The repository for eRMSF is available at https://github.com/pablo-arantes/ermsfkit.

pubs.acs.org

🧠💥 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...

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...

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 👍

Pablo Arantes@pabloarantes.bsky.social · last yr.

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...

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...

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

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...

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...

🚨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)

🚀 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

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

Giulia Palermo@giuliapalermo.bsky.social · 2y ago

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...

Pablo Arantes@pabloarantes.bsky.social · 2y ago

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

Pablo Arantes@pabloarantes.bsky.social · 2y ago

🎓 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! 🌩️🤖

a robot says hey guys in a purple light

ALT: a robot says hey guys in a purple light

media.tenor.com

Just a small lesson for our dear American friends…😉

The New York Times@nytimes.com · 2y ago

Breaking News: Jair Bolsonaro, Brazil’s former president, was charged with overseeing a vast scheme to overturn the 2022 election he lost.

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.

nytimes.com

🚀 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...

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)

Molecular dynamics requires a lot of expert knowledge to set-up and analyze simulations. We set out to automate it with LLM agents: MDCrow!

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/...

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

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”

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 ... 😨

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."

It’s Nazi gestures, Nazi aesthetics, Nazi rhetoric, Nazi symbols. But they’re not Nazis, okay?

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

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

Microsoft researchers introduce MatterGen, a model that can discover new materials tailored to specific needs—like efficient solar cells or CO2 recycling—advancing progress beyond trial-and-error experiments. www.microsoft.com/en-us/resear...

Thank you to everyone for the support and @sokrypton.org for developing the code base which makes these updates much easier to do! Expect BindCraft v2 mid 2025! github.com/martinpacesa...

GitHub - martinpacesa/BindCraft: User friendly and accurate binder design pipeline

User friendly and accurate binder design pipeline. Contribute to martinpacesa/BindCraft development by creating an account on GitHub.

github.com