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Konstantin Korotkov

@korotkov-lab.bsky.social

46 followers 30 following 5 posts

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Konstantin Korotkov @korotkov-lab.bsky.social · 22/01/2025

Hmm, the CCD code option disappeared from the #AlphaFold3 server...

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Konstantin Korotkov @korotkov-lab.bsky.social · 18/01/2025

An update to #AlphaFold3 server. Now, you can add any ligand from the PDB using a CCD Code (up to 2024_10_28). Here is an MPro #SARS-CoV2 inhibitor from PDB 8u9h. The crystal structure is grey, and the #AF3 model is colored by pLDDT.

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Reposted by Konstantin Korotkov

Milot Mirdita @milot.bsky.social · 14/10/2024

Learn how to predict mono-, multi-mers and conformations with the ColabFold-AlphaFold2 protocol now out in @NatureProtocols. Right in time for the Nobel Prize! It covers workflows for beginners and advanced concepts. 🚀https://rdcu.be/dWViQ 📄https://www.nature.com/articles/s41596-024-01060-5 🧬🧶

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Konstantin Korotkov @korotkov-lab.bsky.social · 08/12/2024

Outer product mean should go from MSA to pair representation.

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Reposted by Konstantin Korotkov

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 08/12/2024

David Baker visits all the Rosetta folks after his Nobel lecture. And photo of all three Chemistry laureates - David Baker, Demis Hassabis, and John Jumper. An honor to be here in Stockholm to see this.

Nobel Laureates in Chemistry David Baker, Demis Hassabis, and John Jumper

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Reposted by Konstantin Korotkov

Martin Pacesa @martinpacesa.bsky.social · 08/12/2024

We updated our BindCraft preprint with lots of new exciting results! We release all our binder sequences and models, include more in silico analysis, novel design targets, and present AAV retargeting to specific cell types using de novo binders! www.biorxiv.org/content/10.1...

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Konstantin Korotkov @korotkov-lab.bsky.social · 01/12/2024

Here is the performance of AlphaFold3-server vs. ColabFold-baseline on protein domains. AlphaFold3 is better for the majority of targets. I suspect that the weaker performance of AlphaFold3 in a couple of cases is due to using a reduced database for MSA construction.

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Konstantin Korotkov @korotkov-lab.bsky.social · 01/12/2024

Here is the plot for the protein complex predictions. AlphaFold3 server is an improvement over AlphaFold2 baseline represented by ColabFold. #CASP16

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Reposted by Konstantin Korotkov

Arne Elofsson @handle.invalid · 28/11/2024

#CASP16 program is posted (so you can guess the "winners". Congratulations to Yang and Kihara who seems to have done well in RNA+Proteins. Also congratulations to AF3-server (i.e. me) who was selected to talk (i.e. most people did worse than the server). predictioncenter.org/casp16/doc/C... .

predictioncenter.org

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