SimpleFold: Folding Proteins Is Simpler Than You Think

https://github.com/apple/ml-simplefold

#HackerNews #SimpleFold #Folding #Proteins #AI #Research #Bioinformatics #ProteinFolding #GitHub

💥 Революция в биохимии! ИИ научился предсказывать и даже создавать белки 🧬. AlphaFold и Rosetta меняют всё: от медицины до экологии. Это начало новой эры в науке! 🔬🤖 #AlphaFold #ИИ #биохимия #наука #технологии #NobelPrize #AI #биотех #proteinfolding #DeepMind

Подробнее: https://scientia-et-innovatio.blogspot.com/2025/05/blog-post.html

Dr. Ali Hassanali from the Abdus Salam International Centre for Theoretical Physics (ICTP) is back with a new lecture! This time, Ali discusses the role of amide bonds and dipole moments in the dynamics and stability of protein folding. He investigates how amino acid sequences transform from unfolded to folded states, emphasizing the various interactions that play a crucial role in this fundamental biological process.

🎥 You can access this hashtag#OpenAccess lecture for free on Enabla and engage in meaningful online discussions with Dr. Hassanali and the Enabla community regarding protein folding dynamics and stability: https://enabla.com/pub/1024/about

This is a fantastic opportunity to expand your understanding of protein structure and the factors influencing it, including external conditions like pH and temperature, as well as the impact of post-translational modifications.

#Biophysics #ProteinFolding #MolecularBiology #OpenScience #AminoAcids

👨‍🔬🔍 Apparently, the secret to protein folding was hiding in the 400 Bad Request error all along! Who knew server security policies were the key to solving scientific mysteries? 🧪🔒
https://phys.org/news/2025-03-protein-mystery-core-fractions.html #proteinfolding #serversecurity #scientificbreakthrough #400BadRequest #technologynews #HackerNews #ngated

A protein folding mystery solved: Study explains core packing fractions

https://phys.org/news/2025-03-protein-mystery-core-fractions.html

#HackerNews #proteinfolding #science #research #corepacking #fractions #mysterysolved

https://youtube.com/watch?v=P_fHJIYENdI&si=ECF7pagdnAgEwT4Z

Veritasium just released a great video of #ProteinFolding algorithms and #AlphaFold as part of the story.

The Veritasium team releases some of the best science videos around: accessible, clear and accurate. It's a great service to communicate this breakthrough to everyone.

#ScientificComputing #Bioinformatics #AI #MachineLearning #ScienceCommunication #ProteinDesign

P.S. shame about the anthropomorphic hype at the end

On this note: are you interested in #tech, #selfHosting, #science, #computationalScience, #HPC, #liberatoryTech, or just #POSIX in general but otherwise lack the resources, financial or otherwise? Get in touch with me and we can have a chat about maybe getting you some time. I can't promise when things will be ready or how much I can offer, but.

No generative AI training, please. 'Classic' ML that doesn't generate trash, contribute to surveillance, or rely on stolen data is fine though.

EDIT: please feel free to boost! DMs for initial contact are fine; while I run my server, I do not run yours so just a hello and a general area of interest are all I ask that you put in there. If you feel a project or interest is sensitive we can arrange another chat medium from there. I just wanna get a sense of who you are since I'll be, you know, letting you access the computer sitting in my office lmao.

EDIT 2: I can also specifically help to some degree if you're interested in learning about #computationalChemistry, #proteinFolding, or running a few different types of #simulations.

EDIT 3: If you're interested in writing/deploying/understanding #webDesign, #webTech, etc, that's also possible. I'm not trying to limit anything here, mostly just tagging with what things I know.

EDIT 4: jesus christ Audrey. Anyway, "a sense of who you are" does NOT have to include personally identifying information. I mean much more informal and useful stuff than that, such as what you're interested in and wanna work on. I want you to get to know me a little bit, too, because we'll both need a degree of trust and if you feel you can't trust me then please don't force yourself to.

RE: https://fire.asta.lgbt/notes/a3911f2wi43200mf

How good would any of this AI/NPU processor crap be for protein folding? If it was supported? Folding LOVES GPUs, would it love these other designs?

Also now that I think about it, what about RT and Tensor cores on GPUs too?

Too bad f@h will never be rewritten to leverage any of it it feels like. Unless developments have been happening :>

#FoldingAtHome #ProteinFolding #DistributedComputing #DistributedCompute #BOINC #CUDA

#TerrenceDeacon - #Philosophy of #Biological #Information

https://www.youtube.com/watch?v=KH5p7uFMr3c

#PhilosophyOfBiology #Biology #PhilosophyOfScience #Science #Shannon #Signal #Signals #Complexity #Encoding #DNA #Protein #Chemistry #Folding #ProteinFolding #Evolution #EvolutionaryBiology #CloserToTruth #RobertKuhn

OPINION: Nobel-winning RNA research and AI-driven protein folding models challenge our perceptions of discovery beyond just academia.

https://undark.org/2024/11/07/opinion-nobel-prizes-tell-a-story-about-scientific-discovery/

#NobelPrize2024 #ScienceAndTechnology #Innovation #ScientificDiscovery #AI #MachineLearning #RNAResearch #LifeSciences #PhysicsNobel #ChemistryNobel #ComputationalScience #TechInScience #ScientificInnovation #InterdisciplinaryScience #NonAcademicResearch #FutureOfResearch #EthicsInTech #ProteinFolding #AcademicScience #AIInScience #undark

2024 Nobel Prize - Chemistry: computational chemistry
https://www.nobelprize.org/prizes/chemistry/2024/press-release
* David Baker, UWash: computational protein design
* Demis Hassabis, John Jumper, DeepMind: protein structure prediction

Chemistry Nobel to dev. of AlphaFold AI that predicts protein structures
https://www.nature.com/articles/d41586-024-03214-7

* https://old.reddit.com/r/MachineLearning/comments/1fznxyr/n_the_2024_nobel_prize_in_chemistry_goes_to_the
* https://www.technologyreview.com/2024/10/09/1105335/google-deepmind-wins-joint-nobel-prize-in-chemistry-for-protein-prediction-ai
* https://news.ycombinator.com/item?id=41775463

#2024Nobel #ComputationalBiology #ProteinDesign #ProteinFolding #AI #LLM #AlphaFold #AlphaFold2 #DeepMind #bioinformatics

Nobel Prize in Chemistry 2024:

David Baker, USA, is honored for his work in computational protein design,

the other half is shared by Demis Hassabis and John M. Jumper, both UK, for their contributions to protein structure prediction

https://www.chemistryviews.org/nobel-prize-in-chemistry-2024/

#chemistry #chemistryviews #chemviews #chemiverse #nobelprize2024 #2024nobelprize #chemistrynobelprize #nobelprizeinchemistry #proteinfolding #biochemistry #ai

AlphaProteo generates novel proteins for biology and health research
https://deepmind.google/discover/blog/alphaproteo-generates-novel-proteins-for-biology-and-health-research
https://news.ycombinator.com/item?id=41457331

* Google DeepMind
* AI system designs proteins that successfully bind to target molecules
* potential for advancing drug design, disease understanding

#ComputationalBiology #ProteinFolding #AlphaFold #AlphaProteo #SyntheticBiology #ProteinProteinInteractions #ProteinDrugInteractins #PDI #interactome #DeepMind #AI

Biologists are so ridiculous. They’re folding proteins, and they’re telling you they need supercomputers for that. I’ll have you know I just folded a fitted sheet, with my bare hands. #Biology #ProteinFolding

#AlanLove - #PhilosophyOfMolecularBiology & #Genes

https://www.youtube.com/watch?v=btP7EFuVxxs

#Philosophy #PhilosophyOfBiology #Biology #PhilosophyOfScience #Science #Genetics #Evolution #Gene #Classification #Protein #Proteins #ProteinFolding #AlphaFold #SideEffects #CloserToTruth #RobertKuhn

3-JUL-2024
Do genes-in-pieces code for proteins that fold in pieces?

https://www.eurekalert.org/news-releases/1050362
the method used is called #FrustrationAnalysis - I like that.
#science #ProteinFolding #nanoworld

"This is the story of how Jumper’s team at Google DeepMind pulled off their coup in protein science, and what it means for the future of artificial intelligence in biology."

https://www.quantamagazine.org/how-ai-revolutionized-protein-science-but-didnt-end-it-20240626/

#MachineLearning #Biology #Proteins #GoogleDeepMind #ProteinFolding

In the prediction of complexes with drug like molecules, the #AlphaFold3 vs Docking testing was not set-up fairly, argues Oleg Trott in this interesting point ⬇️

https://www.lesswrong.com/posts/D9yYmL6KPq7dcNSKE/i-m-a-bit-skeptical-of-alphafold-3

#drugdesign #machinelearning #artificialintelligence #ProteinFolding

2/

AlphaFold 3 predicts the structure and interactions of all of life’s molecules
https://blog.google/technology/ai/google-deepmind-isomorphic-alphafold-3-ai-model/
https://news.ycombinator.com/item?id=40298927

Introducing AlphaFold 3, a new AI model developed by Google DeepMind and Isomorphic Labs. By accurately predicting the structure of proteins, DNA, RNA, ligands and more, and how they interact, we hope it will transform our understanding of the biological world and drug discovery.

#AlphaFold #AI #ProteinFolding #DeepMind #ComputationalBiology #ProteinInteractions

1/

Google DeepMind’s new AlphaFold can model a much larger slice of biological life
AlphaFold 3 can predict how DNA, RNA and other molecules interact, further cementing its leading role in drug discovery and research. Who will benefit?
https://www.technologyreview.com/2024/05/08/1092183/google-deepminds-new-alphafold-can-model-a-much-larger-slice-of-biological-life/

Comment: revolutionary

#AlphaFold #AI #ProteinFolding #DeepMind #ComputationalBiology #ProteinInteractions