Guilherme M. Arantes
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garantes.bsky.social
Guilherme M. Arantes
@garantes.bsky.social
Professor & Scientist @uspoficial.bsky.social 🇧🇷. Visiting @mit.edu. Scholar @ieausp.bsky.social. Computational (bio)chemistry and biophysics.

Web: http://gaznevada.iq.usp.br
🐦 : x.com/ArantesLab
🎵 : www.dinamicas.art.br
Pinned
🚀 Benchmark paper out!

How well do DFT, semiempirical & ML methods model proton transfer?
✅ DFT performs well, except with N-groups
❌ Pure ML struggles (though ORB v3 shows big gains)
🔥 PM6-ML Δ-learning excels, even in QM/MM setups!

Check it out: pubs.acs.org/doi/10.1021/...
Benchmark of Approximate Quantum Chemical and Machine Learning Potentials for Biochemical Proton Transfer Reactions
Proton transfer reactions are among the most common chemical transformations and are central to enzymatic catalysis and bioenergetic processes. Their mechanisms are often investigated using DFT or approximate quantum chemical methods, whose accuracy directly impacts the reliability of the simulations. Here, a comprehensive set of semiempirical molecular orbital and tight-binding DFT approaches, along with recently developed machine learning (ML) potentials, are benchmarked against high-level MP2 reference data for a curated set of proton transfer reactions representative of biochemical systems. Relative energies, geometries, and dipole moments are evaluated for isolated reactions. Microsolvated reactions are also simulated using a hybrid QM/MM partition. Traditional DFT methods offer high accuracy in general but show markedly larger deviations for proton transfers involving nitrogen-containing groups. Among approximate models, RM1, PM6, PM7, DFTB2-NH, DFTB3, and GFN2-xTB show reasonable accuracy across properties, though their performance varies by chemical group. The ML-corrected (Δ-learning) model PM6-ML improves accuracy for all properties and chemical groups and transfers well to QM/MM simulations. Conversely, standalone ML potentials perform poorly for most reactions. These results provide a basis for evaluating approximate methods and selecting potentials for proton transfer simulations in complex environments.
pubs.acs.org
Reposted by Guilherme M. Arantes
e digo mais: servidores estrangeiros em solo brasileiro não só não garante soberania como pode ser cavalo de troia CONTRA nossa soberania territorial.

quem acha exagero é pq não conhece a ideologia neoreacionária, nem sabe como pensam o Thiel, o Altman e outros "fundadores" de empresas de IA.
Serpro: Brasil está vendendo sua soberania digital? | Outras Palavras
Em troca de “pacotes de nuvem”, empresa pública entrega dados sensíveis -- do SUS à Receita Federal – para as big techs. Há o risco dos EUA também acessá-los. Resgatar princípios do software livre, ho...
outraspalavras.net
November 6, 2025 at 8:55 PM
Reposted by Guilherme M. Arantes
Micrograd: a pedagogical implementation of neural networks using a reverse-mode automatic differentiation engine.

https://hyperdoc.khinsen.net/94FE4-micrograd

I have written this as a real-life example of explorable explanations in HyperDoc.

Feedback welcome at […]
Original post on scholar.social
scholar.social
November 3, 2025 at 1:21 PM
Reposted by Guilherme M. Arantes
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE

Artificial Intelligence Driven protein Estimation (AIDE), enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods

doi.org/10.1093/bioi...
October 29, 2025 at 7:45 AM
Reposted by Guilherme M. Arantes
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
Reposted by Guilherme M. Arantes
A biomimética é considerada uma área estratégica para a agenda de inovação e sustentabilidade. Encontro no dia 29 de outubro, às 8h30, destina-se a difundir como a ciência e a comunidade científica internacional têm abordado o tema. Informações: www.iea.usp.br/eventos/biologia-evolutiva-biomimetica.
October 24, 2025 at 5:15 PM
Reposted by Guilherme M. Arantes
Structures of rotary ATP synthase from Thermus thermophilus during proton powered ATP synthesis | Science Advances www.science.org/doi/10.1126/...
Structures of rotary ATP synthase from Thermus thermophilus during proton powered ATP synthesis
Cryo-EM snapshots of the ATP synthase driven by proton motive force reveal the torsional deformation during ATP synthesis.
www.science.org
October 18, 2025 at 7:42 PM
Reposted by Guilherme M. Arantes
Join us in Room 181, Building 68 @mit.edu on October 22nd 2025 @ 7pm EDT to see @grocklin.bsky.social present a mind blowing amount of data and learn what becomes possible at this scale

"Predicting protein folding stability and aggregation propensity using large-scale experiments"

bpdmc.org
schedule
introduction and membership Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...
bpdmc.org
October 17, 2025 at 8:27 PM
Reposted by Guilherme M. Arantes
I wrote a blog post about the future of structural bioinformatics.

Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?

Let me know what you think.

jgreener64.github.io/posts/struct...
Where next for structural bioinformatics?
jgreener64.github.io
October 15, 2025 at 2:16 PM
Last week at the University of Tennessee, I presented my research on Machine Learning and Quantum Chemistry potentials. It was a great discussion at the symposium about the future of MLIP and approximate QC methods! 😊 😎 #compchem #ai4science

www.smlqc2025.com/p/invited-sp...
October 14, 2025 at 2:24 PM
Reposted by Guilherme M. Arantes
I finished my estimate on required compute to make an atomic-resolution virtual cell: 10^38 FLOPs to simulate a human cell for 1 day. We should be able to do this simulation in 2074 using 200 TW of power. 1/3
September 26, 2025 at 3:19 PM
Reposted by Guilherme M. Arantes
The future of medicine is about preventing the major diseases from ever showing up. Primary prevention.
erictopol.substack.com/p/dawn-of-a-...
Dawn of A New Era of Primary Prevention in Medicine
Recent groundbreaking reports highlight our newfound potential to prevent diseases
erictopol.substack.com
September 24, 2025 at 7:01 PM
Reposted by Guilherme M. Arantes
MPF apresenta alegações final para cancelamento das outorgas da Jovem Pan

Por atuar para desinformar os ouvintes e, além da perda das outorgas, emissora deve ser condenada a pagar R$ 13,4 milhões por danos morais coletivos

jornalggn.com.br/justica-2/mp...
MPF apresenta alegações final para cancelamento das outorgas da Jovem Pan
Por atuar para desinformar os ouvintes e, além da perda das outorgas, emissora deve ser condenada a pagar R$ 13,4 milhões por danos morais coletivos
jornalggn.com.br
September 15, 2025 at 6:16 PM
Reposted by Guilherme M. Arantes
Minicurso online no dia 23 de setembro, às 19h, tratará dos desafios epistêmicos colocados pela inteligência artificial na educação e suas implicações para o currículo, num contexto marcado pela plataformização do ensino e pela vigilância de dados. Inscrições: forms.gle/RZFWF3wAyzmVFYv26.
September 11, 2025 at 1:17 PM
Reposted by Guilherme M. Arantes
The latest @livecomsjournal.bsky.social tutorial "Molecular Dynamics: From Basics to Application" by Vollmers, Chen et al is out now! doi.org/10.33011/liv...

It includes comprehensive MD tutorials in GROMACS, covering forcefields, thermodynamic ensembles, long-range electrostatics and much more!
September 9, 2025 at 12:19 PM
Reposted by Guilherme M. Arantes
We're looking for a mass spec expert to join our team at @aiproteins.com! This position is ideal for a freshly-minted PhD grad (or someone who will graduate within the next 6 months or less), or a rockstar scientist who earned their skills on the job in biotech
September 3, 2025 at 5:47 PM
Reposted by Guilherme M. Arantes
Pesquisadores da USP e da Amazon Web Services criam modelo de linguagem com IA para acelerar decisões judiciais na saúde, reduzindo prazos e apoiando juízes com base em evidências científicas
Modelo de linguagem baseado em IA pretende acelerar decisões judiciais na saúde
Software desenvolvido por pesquisadores da USP, em parceria com a Amazon, pode ajudar juízes na análise de pareceres técnicos relacionados à aprovação de medicamentos
jornal.usp.br
September 3, 2025 at 3:11 PM
Reposted by Guilherme M. Arantes
One take-away from #benzon25 is that while we now have great structure prediction and sequence design models, many (most?) problems actually require thermodynamic models and that extracting and tuning thermodynamics from structure/sequence remains very hard.
September 2, 2025 at 1:33 PM
🎥 Neste videocast produzido junto do @ieausp.bsky.social, tive uma conversa inspiradora com o Anderson Soares (UFG), @alexandre-cf.bsky.social e o @cdbahl.com sobre como a IA está moldando o futuro da biologia e da saúde humana. Assista aqui 👉 www.youtube.com/watch?v=qQbZ...
Inteligência Artificial Aplicada às Ciências da Vida
YouTube video by Instituto de Estudos Avançados da USP
www.youtube.com
September 1, 2025 at 4:00 AM
Reposted by Guilherme M. Arantes
Coordenado pelo bioquímico Guilherme Menegon Arantes quando participou do Programa Ano Sabático do IEA, videocast discute como a IA pode transformar a biologia e a medicina e o que ela já possibilita para melhorar a qualidade de vida: www.youtube.com/watch?v=qQbZ_Y7o-Yg&t=11s.
@garantes.bsky.social
Inteligência Artificial Aplicada às Ciências da Vida
YouTube video by Instituto de Estudos Avançados da USP
www.youtube.com
August 29, 2025 at 2:48 PM
Reposted by Guilherme M. Arantes
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...
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
Reposted by Guilherme M. Arantes
This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...
Protein language models reveal evolutionary constraints on synonymous codon choice
Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...
www.biorxiv.org
August 7, 2025 at 8:29 AM
Reposted by Guilherme M. Arantes
If you’re interested in learning more about protein folding and misfolding, I’ve created a convenient reading list with a few essential papers:

scholar.google.com/citations?us...

scholar.google.com/citations?us...
August 6, 2025 at 7:01 PM
Reposted by Guilherme M. Arantes
Setor público gasta bilhões com Big Techs ao invés de ciência nacional
jornalggn.com.br/ciencia/seto...
Setor público gasta bilhões com Big Techs ao invés de ciência nacional
Com valor despendido, nos últimos dez anos, seria possível construir e inaugurar pelo menos 86 data centers de alto padrão no Brasil.
jornalggn.com.br
August 6, 2025 at 2:21 PM
Reposted by Guilherme M. Arantes
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🧵
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