#alphafold

Почувствуй себя рибосомой. Как устроен современный дизайн белков

Привет! Это Маша Синдеева, научный сотрудник группы дизайна белков AIRI. Основное направление нашей группы — это разработка ИИ‑моделей для задач, связанных с дизайном белков. В этом посте я постараюсь рассказать о том, что такое белки, как устроен процесс их дизайна, и как с этим может помочь наша новая статья AFToolkit: a framework for molecular modeling of proteins with AlphaFold‑derived representations , которая вышла в журнале Briefings in Bioinformatics, и которую мы написали вместе с ребятами из группы органической химии AIRI.

https://habr.com/ru/companies/airi/articles/933238/

#биоинформатика #дизайн_белков #AlphaFold

What is the key idea of #AlphaFold? There isn't one. #ismbeccb2025

After #AlphaFold 1, the team tried to work without evolutionary information, to learn what they could do from physics. Accuracy was terrible (John Jumper’s words), but they learned a lot by changing the approach. Use the plausible but false structures to create a space of possibilities to explore iteratively. “Kind of surprisingly, it started to work.” #ismbeccb2025

First keynote of #ismbeccb2025: John Jumper, first but not last surely with #MachineLearning #AI at the center.
We all know about #AlphaFold, John will tell us about the challenges along the way. Good start! “Evolution is important”

AI for science, drug discovery to have ‘greatest impact’, says Nvidia’s Huang https://www.byteseu.com/1204271/ #AI #AIForScience #Alibaba #AlibabaCloud #AlphaFold #Beijing #biology #ByteDance #China #ChinaInternationalSupplyChainExpo #DamoAcademy #DrugDiscovery #JensenHuang #Science #WangJian

CASP, the protein structure competition that rocketed AlphaFold to fame and a Nobel, is losing its NIH funding.

David Baker on how CASP impacted his career (and Nobel Prize), and what's the latest on CASP's funding status:

https://www.statnews.com/2025/07/16/casp-protein-structure-competition-of-alphafold-fame-nearing-deal-to-replace-lost-nih-funding/

#health #healthcare #medicine #science #research #ai #artificialintelligence #casp #nih #biology #nobelprize #alphafold

Interesting post on the important limitations of #AlphaFold in helping us to truly understand protein structure and function.

Sorry, the post is on substack.

https://clauswilke.substack.com/p/no-alphafold-has-not-completely-solved

Oh man. Ich weiß auch nicht, warum die Betreuung von Promovierenden so viel Spaß macht.

Aber das gemeinsame Brainstorming und Probleme lösen, das fetzt einfach total.

Hat alles voll die Sogwirkung. Und mit jedem Paper und weiteren Tool tut sich direkt ein neues Rabbit Hole auf. 🫣

Aktuell betreue ich eine Doktorandin, die Proteinsimulation macht.

#Gromacs #Alphafold #PyMOL

https://www.europesays.com/uk/254836/ The Unlikely Reasonableness of AI-Augmented HPC #AI #AlphaFold #Biology #Chemistry #Computing #LLMs #LQMs #OpenFold #Physics #Technology #UK #UnitedKingdom #Weather

https://www.europesays.com/2233124/ Hong Kong start-up IntelliGen AI aims to challenge Google DeepMind in drug discovery #Accenture #AI #AlphaFold #ArtificialIntelligence #Baidu #ByteDance #China #DeepMind #DrugDiscovery #FudanUniversity #FutureCapital #google #HongKong #IntelliGenAI #IsomorphicLabs #RonaldSun

Charité study analyzes 400 million years of enzyme evolution!

With the aid of #AlphaFold AI, a research team has decoded the laws according to which #enzymes - which catalyze chemical reactions in all living things - evolve. The results, which have now been published in the scientific journal #Nature, are relevant to the development of new antibiotics, for example.

https://www.charite.de/en/service/press_reports/artikel/detail/charite_study_analyzes_400_million_years_of_enzyme_evolution

#CharitéPaper #ScienceMastodon #science #research #CharitéBerlin #AI #CharitéBiochemistry #biology

Charité-Studie analysiert 400 Millionen Jahre Enzym-Evolution!

Mithilfe der #AlphaFold-KI hat ein Forschungsteam die Gesetzmäßigkeiten entschlüsselt, nach denen sich #Enzyme – die chemische Reaktionen in allen Lebewesen beschleunigen – weiterentwickeln. Die jetzt im Fachmagazin #Nature veröffentlichten Ergebnisse sind beispielsweise für die Entwicklung neuer Antibiotika relevant.

https://www.charite.de/service/pressemitteilung/artikel/detail/charite_studie_analysiert_400_millionen_jahre_enzym_evolution

#CharitéPaper #ScienceMastodon #Forschung #Wissenschaft #CharitéBerlin #KI

"In my view this day will not come soon,
but when it does come the X-ray crystallographers can go out of business,
perhaps with a certain sense of relief, and it will also be possible to discuss the structures of many important proteins which cannot be crystallized and therefore lie outside the crystallographer’s purview."

One wonders whether #Google's #Isomorphic labs were named after the mathematical modelling, or the isomorphous replacement technique pioneered here?

#AlphaFold #biotech #AI

Eines der besten Bücher zur organischen Chemie wenn ihr mich fragt.

Brauche ich gerade wieder um mein Wissen über Reaktionsmechanismen aufzufrischen.

Ich mache gerade Proteinfaltung mit #Alphafold und muss dann mit #PyMOL das Substrat in der Tasche des Enzyms bewerten bzw. möchte verstehen, welche Aminosäure genau wo angreift.

Dr Ron Vale

The Impact of AlphaFold on Cell Biology

Cellular Interfaces Seminar

Friday 20 June, 11.15am-12.15pm, GLT2, Medical School Building

Note the change of venue!

#CellBiology #AlphaFold #biophysics

Tomorrow we are hosting a talk from Ron Vale:

The Impact of AlphaFold on Cell Biology
Dr Ron Vale, Emeritus Professor of Cellular and Molecular Pharmacology, University of California

Cellular Interfaces Seminar
Friday 20 June, 11.15am-12.15pm, A151/MBU, Medical School Building

#CellBiology #AlphaFold #biophysics

[Перевод] Потеря работы из-за ИИ: насколько реальна угроза? Мнение Демиса Хассабиса

Имя Демиса Хассабиса — синоним амбициозных проектов в области ИИ. От разработки легендарной игры Theme Park до создания AlphaFold, решившей «нобелевскую» задачу биологии, и теперь — к AGI , искусственному интеллекту уровня человека. Глава DeepMind утверждает: шанс увидеть AGI в ближайшее десятилетие — 50/50. Этот прогноз одновременно восхищает и пугает. Ведь за ним маячит призрак массовой потери работы из‑за ИИ. Насколько реален апокалипсис профессий? И есть ли свет в конце тоннеля общего искусственного интеллекта? Погружаемся в мысли одного из главных архитекторов нашего будущего.

https://habr.com/ru/companies/bothub/articles/919718/

#демис_хассабис #agi #deepmind #google #alphafold #го #шахматы #ai_mode #ai_overviews #колонизация_космоса

Improved 3D prediction from #alphafold (2/3) . Result from #casp15 Deep-learning-based single-dome and multidomain protein structure prediction with D-I-TASSER. Nature Biotechnology https://zhanggroup.org/D-I-TASSER/help.html#casp15

What role does protein design play in advancing next-gen optogenetic tools?

Protein design accelerates the development and application of optogenetic tools. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.02.014

CSBJ: https://www.csbj.org/

#Optogenetics #ProteinEngineering #Neuroscience #AlphaFold #ProteinDesign #SyntheticBiology

Microsoft’s New BioEmu-1 AI Model Can Predict How Proteins Move and Change

#AI #BioEmu1 #Microsoft #MicrosoftResearch #DiffusionModels #BioScience #Science #AIResearch #Alphafold #BigTech

https://winbuzzer.com/2025/02/28/microsofts-new-bioemu-1-ai-model-can-predict-how-proteins-move-and-change-xcxwbn/