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Marian Novotny

@majek.bsky.social

Proud dad, structural bioinformatician, cook, birdwatcher and skater

37 Posts311 Follower225 Folgt
Pedro Beltrao@pedrobeltrao.bsky.social · 3w ago

Anthropic has used Claude to optimise structure prediction and design code to improve speed and memory efficiency. 2-3X speed improvements on AF3, 5X on OF3, 5X on BindCraft low memory modes to model large assemblies. All released as open source www.anthropic.com/research/cla...

How Claude is uplifting biomolecular modeling

Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.

anthropic.com

Pedro Beltrao@pedrobeltrao.bsky.social · last yr.

Great work from Horia Todor in Carol Gross's lab showing it's possible to predict complexes in "competition" pools in AF3 resulting in the first all-by-all prediction for a species. After length correcting the ipTM score predicts well known interactions and correlating ipTM vectors also has value.

bioRxiv SysBio@biorxiv-sysbio.bsky.social · last yr.

Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3 https://www.biorxiv.org/content/10.1101/2025.07.01.662654v1

Marian Novotny@majek.bsky.social · last yr.

P2Rank has a new version - you can even see a ligand bound to the identified pocket now - please , check it out and look at our NAR paper for a summary of the upgrades

Radoslav Krivak@rdkbio.bsky.social · last yr.

🚀 Our paper on the updated PrankWeb, a web app for protein binding site prediction using P2Rank, is out in @narjournal.bsky.social. Now with docking integration! 👨‍💻 Try it: prankweb.cz 📄 Paper: doi.org/10.1093/nar/... 💻 GitHub: github.com/cusbg/prankweb Developed at @cusbg.bsky.social

Screenshot of PrankWeb.
Deník N@denikn.cz · last yr.

„Hledání života ve vesmíru je pro mě asi největší vědecké dobrodružství,“ říká jedna z nejúspěšnějších českých vědkyň, biochemička a astrobioložka Klára Hlouchová. Zkoumá otázky původu a evoluce proteinů. Co ještě není, a co už je schopno života?

Nález života ve vesmíru by s námi mohl pěkně zamávat, říká astrobioložka. Zkoumá vznik života i slepé uličky

Co ještě není, a co už je schopno života? A jak by mohl vypadat život ve vesmíru? Biochemička a astrobioložka Klára Hlouchová zkoumá otázky původu a evoluce proteinů. A otázky života, vesmíru a tak…

denikn.cz

Marian Novotny@majek.bsky.social · 2y ago

Things are often obvious, but sometimes less so. It is true also for small things like ligand-binding sites. In this work, our @cusbg.bsky.social group presents a new dataset designed for cryptic-binding site predictons - happy, to be part of this: academic.oup.com/bioinformati...

CryptoBench: cryptic protein–ligand binding sites dataset and benchmark

AbstractMotivation. Structure-based methods for detecting protein–ligand binding sites play a crucial role in various domains, from fundamental research to

academic.oup.com

Česká společnost ornitologická@birdlife.cz · 2y ago

🪶Nečekané a vzácné pozorování pelikána bílého ve čtvrtek v ptačím parku Kosteliska na Hodonínsku. Pták byl v dobré kondici, bez chovatelských kroužků a často ladně přeletoval a kroužil. Jedná se již o 209. ptačí druh pozorovaný v ptačím parku ČSO Kosteliska. Foto: Ondřej Ryška

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estella newcombe@estellaan.bsky.social · 2y ago

We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered??? www.nature.com/articles/s41...

Stereochemistry in the disorder–order continuum of protein interactions - Nature

Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.

nature.com