#alphafold3 — Public Fediverse posts

AI protein-prediction tool AlphaFold3 is now more open https://www.nature.com/articles/d41586-024-03708-4 #science #openscience #reproducibility #alphafold3

💡 AI can predict protein structures — but can it predict how they behave?

🔗 AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.015

📚 CSBJ: https://www.csbj.org/

#AlphaFold3 #ProteinDesign #MolecularModeling #ComputationalBiology #StructuralBiology #Thermodynamics #ProteinProteinInteractions #Bioinformatics

💡 AI can predict protein structures — but can it predict how they behave?

🔗 AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.015

📚 CSBJ: https://www.csbj.org/

#AlphaFold3 #ProteinDesign #MolecularModeling #ComputationalBiology #StructuralBiology #Thermodynamics #ProteinProteinInteractions #Bioinformatics

💡 AI can predict protein structures — but can it predict how they behave?

🔗 AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.015

📚 CSBJ: https://www.csbj.org/

#AlphaFold3 #ProteinDesign #MolecularModeling #ComputationalBiology #StructuralBiology #Thermodynamics #ProteinProteinInteractions #Bioinformatics

💡 AI can predict protein structures — but can it predict how they behave?

🔗 AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.015

📚 CSBJ: https://www.csbj.org/

#AlphaFold3 #ProteinDesign #MolecularModeling #ComputationalBiology #StructuralBiology #Thermodynamics #ProteinProteinInteractions #Bioinformatics

💡 AI can predict protein structures — but can it predict how they behave?

🔗 AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.015

📚 CSBJ: https://www.csbj.org/

#AlphaFold3 #ProteinDesign #MolecularModeling #ComputationalBiology #StructuralBiology #Thermodynamics #ProteinProteinInteractions #Bioinformatics

🚀 GenAI isn’t science fiction anymore. From GPT-4o aiding the blind to AlphaFold 3 cutting drug discovery timelines by 50%, the future is already here.

👁️ Explore how 4 GenAI breakthroughs are transforming vision, video, medicine, and work—plus what comes next.

#GenAI #GPT4o #Sora #AlphaFold3 #AIethics #AgenticAI #AIin2025

🔗
https://medium.com/@rogt.x1997/4-genai-breakthroughs-solving-20b-problems-from-gpt-4o-to-alphafold-3-f977120f65ef

DeepMind Tightens Control Over AI Research to Guard Google’s Competitive Advantage

#AI #DeepMind #GoogleAI #GeminiAI #AIresearch #AlphaGeometry #AlphaFold3 #AGI #AIsecrecy #RoboticsAI #TxGemma #AIethics #OpenScience #LLMs

https://winbuzzer.com/2025/04/01/deepmind-tightens-control-over-ai-research-to-guard-googles-competitive-advantage-xcxwbn/

Protip: If you specify an AlphaFold 3 ligand by ccdCode, it has to have brackets around it. If it doesn't, each individual element of the string will be evaluated as a code which is probably not what you want.

Wrong:

"ccdCodes": "C2E"
ValueError: Unknown residue type 2

Right:
"ccdCodes": ["C2E"]

#AlphaFold3

so now deepmind has gone and released alphafold3 code as well. must have been feeling the competition.

source code here: https://github.com/google-deepmind/alphafold3

🧪🧬🖥️
#alphafold3 #bioinformatics #ai #ml

@xtaldave @graemewinter I was just preparing my "6 month are over"-Tweet to be released tomorrow and found this: https://github.com/google-deepmind/alphafold3 So google did hold their promise with 48h to spare 😅 It will take me time to implement it, but I cannot wait to see it for myself! #AlphaFold3

#DeepMind finally released the code of #AlphaFold3! But with very restrictive conditions to use the model weights... And anyway, I wonder which academic lab has the hardware to run it, beside David Baker's lab maybe...

#StructuralBiology #StructuralBioinformatics

Announcement: https://doi.org/10.1038/d41586-024-03708-4

Code: https://github.com/google-deepmind/alphafold3

Hardware requirements: https://github.com/google-deepmind/alphafold3/blob/main/docs/performance.md#accelerator-hardware-requirements

Form to request authorization to use the model weights: https://forms.gle/svvpY4u2jsHEwWYS6

So, Bytedance, the people behind tiktok have created protenIx, a pytorch recreation of alphafold 3

https://github.com/bytedance/Protenix

🧪🧬🖥️ #alphafold3 #ai #alphafold

Avec mon collègue @AntoineTaly, on a écrit un petit truc pour médecine/sciences pour présenter rapidement les améliorations et restrictions d'#alphafold3 par rapport à #alphafold2

https://www.medecinesciences.org/en/articles/medsci/abs/2024/08/msc240162/msc240162.html

Does anyone using #Alphafold3 with multiple copies of the same sequence ever get this problem? Basically laying chains exactly on top of each other…in this house we obey the Pauli exclusion principle!

Is anyone doing structure prediction with #AlphaFold3 figured out an easy way to do the relaxation step that Colabfold did? I'm looking into OpenMM and Amber, and making some progress, but it seems like it will be very difficult to make it work when phosphoresidues, ions, or anything else besides standard amino acid residues are included.

#proteins #structuralbiology #moleculardynamics

Bringing this over from twitter: https://arxiv.org/abs/2408.16975 - A free and open source of #AlphaFold3 - If this stands true, that would be amazing. 🤞

Petite histoire du #Logiciel #AlphaFold3 ou comment l’absence de #CodeOuvert conduit à refaire ce qui existe déjà

➡️ https://openscience.pasteur.fr/2024/06/20/petite-histoire-du-logiciel-alphafold3-ou-comment-labsence-de-code-ouvert-conduit-a-refaire-ce-qui-existe-deja/

hi community,

AlphaFold 3 provides a breakthrough in molecular biology and data science in general. However, its environmental impact is not known. Any sources giving the impact of an inference in eq CO2 ?

#WorldEnvironmentDay #WorldEnvironmentDay2024
#AlphaFold #AlphaFold3

I tried helping one of our #HPC users running #Alphafold . She had some weird issues from logging in to starting a job, and then the new release of #alphafold3 came out. I packed and provided a container and a sample script.

Then I missed following up. Now she wrote me:

> Thank you for coming back to me about it. The issue is solved, I am now using the new alphafold server which is really easy and fast to use. https://golgi.sandbox.google.com/about

Understandably, our service is bad for a number of reasons.

@petersuber See the open letter by scientists calling out DeepMind and Nature on not releasing the code of AlphaFold3: https://zenodo.org/records/11206103

Among other things, they write that one of the letter writers was actually a referee and did not get access to the code, despite repeated requests. They point out that access is so limited that key claims cannot be tested:
"The high-profile publication advertises capabilities that remain locked behind the doors of the parent company".

#alphafold3

Todas con todas. Dejad de imaginarlo. Ya existe. Ya es una realidad. Este es el nuevo regalo de @googledeepmind La fuerza bruta computacional, millones de datos de entrenamiento y la IA puestas al servicio de entender las interacciones moleculares. El resultado se llama #AlphaFold3 publicado en @nature
https://www.nature.com/articles/s41586-024-07487-w

#AlphaFold3: Googles KI sagt Struktur aller Moleküle voraus | heise online https://www.heise.de/news/AlphaFold-3-Googles-KI-sagt-Struktur-aller-Molekuele-voraus-9713361.html #DigitalHealth #Digitalisierung #digitalization #ArtificialIntelligence #OpenSource

🧠 In un articolo pubblicato su Nature, #Google DeepMind presenta #AlphaFold3.
👉 Un modello rivoluzionario in grado di prevedere la struttura e le interazioni di tutte le "molecole della vita", con una precisione senza precedenti.
⭐ Gli scienziati potranno accedere gratuitamente a quasi tutte le funzionalità del sistema gratuitamente.

🔗 https://blog.google/technology/ai/google-deepmind-isomorphic-alphafold-3-ai-model/

#AI #GenAI #GenerativeAI #IntelligenzaArtificiale 

#AlphaFold3 is here.
https://blog.google/technology/ai/google-deepmind-isomorphic-alphafold-3-ai-model/
#AI #google

Google #DeepMind’s ‘leap forward’ in #AI could unlock secrets of biology

#Alphafold3 #proteins #RNA

https://www.theguardian.com/science/article/2024/may/08/google-deepmind-ai-biology-alphafold

AlphaFold3 is now available and looks like it can handle all molecule interactions!

Webserver: https://golgi.sandbox.google.com/about
Paper: https://www.nature.com/articles/s41586-024-07487-w

#AlphaFold #AlphaFold3 #ProteinStructure