Guilherme M. Arantes
@garantes.bsky.social
2.3K followers 340 following 120 posts
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
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garantes.bsky.social
🚀 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
garantes.bsky.social
I agree PCET is tough but simple PT is isogyric, so shouldn't be hard for most QC methods
Reposted by Guilherme M. Arantes
andrew.diffuse.one
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
garantes.bsky.social
Nice work Ramon! Good to see you doing some structure prediction too!
garantes.bsky.social
Nice work! BtW, have you parameterized cardiolipin for CpHMD in Gromacs with the charmm36.ff ?
Reposted by Guilherme M. Arantes
2cotrim.bsky.social
o ronaldinho virou uma fusão de miles davis e stevie wonder
ronaldinho gaúcho usando um terno risca de giz, óculos escuros e tiara no prêmio bola de ouro
Reposted by Guilherme M. Arantes
luisnassif.bsky.social
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
Reposted by Guilherme M. Arantes
ieausp.bsky.social
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.
Reposted by Guilherme M. Arantes
livecomsjournal.bsky.social
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!
Reposted by Guilherme M. Arantes
cdbahl.com
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
Reposted by Guilherme M. Arantes
garantes.bsky.social
(bio)comp ppl will now have to look into some statistical mechanics...
Reposted by Guilherme M. Arantes
lindorfflarsen.bsky.social
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.
garantes.bsky.social
🎥 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
garantes.bsky.social
Sim, mas aqui é feriado!
Reposted by Guilherme M. Arantes
ieausp.bsky.social
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
Reposted by Guilherme M. Arantes
pabloarantes.bsky.social
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
Reposted by Guilherme M. Arantes
lianafaye.bsky.social
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
garantes.bsky.social
It was a great conference! Congrats to all involved! 👏
Reposted by Guilherme M. Arantes
lindorfflarsen.bsky.social
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...
Reposted by Guilherme M. Arantes
fraserlab.com
Protein-ligand complexes are all the rage with OpenBind+other efforts launching

3 amazing papers describing 229 protein-ligand structures just dropped in @actacrystd.iucr.org

A tremendous teaching text, but I disagree on the discussed potential for misuse. Read more

fraserlab.com/2025/07/29/E...
Embrace the Mess
This is the official web page for the James Fraser Lab at UCSF.
fraserlab.com
garantes.bsky.social
While I am all for more connections, the route from Logan -> SL1 -> South S. -> Red line is already great. Don't see how this one via Norrth would help. But a plus would be if they tunnel/hide the track that passes through MIT (as we can hear when the train passes in the Port area and around...)