Maxim Tsenkov
@mitsenkov.bsky.social
Bioinformagician at AlphaFold DB 🧙🏼♂️| PDBe team at EMBL-EBI | Helping you unlock the magic of AlphaFold DB with new features and tools 🔬✨ | Proud LEGO enthusiast 🧱 | Turning data into discoveries!
Yes, only AF2, not AF3. Unchanged models would be the same as 2021, since the settings used here are identical to every release we've had before, and MSAs cached from previous runs for unchanged sequences. Also the sequence databases also remain the same. So the entire db is consistent throughout.
October 23, 2025 at 1:15 PM
Yes, only AF2, not AF3. Unchanged models would be the same as 2021, since the settings used here are identical to every release we've had before, and MSAs cached from previous runs for unchanged sequences. Also the sequence databases also remain the same. So the entire db is consistent throughout.
Sorry to keep you waiting Max! We got overwhelmed with questions on this release. So we wrote another post to clarify some of these queries here – bsky.app/profile/mits...
You probably heard about the last major release at #AlphaFold Database two weeks ago. We hope this new post will cover any further questions about the details of the release. If you have any other questions, please do reply here or email us your queries – afdbhelp@ebi.ac.uk
AlphaFold DB v6 (synced with UniProt 2025_03) is live! Here are the details:
Totals v4 → v6: 241,070,489 entries.
Since v4: +65,711,653 added, 39,324,993 removed, 276,539 changed (in sequence), 175,082,297 unchanged (metadata refresh, relabelled v6). Details 👇
Totals v4 → v6: 241,070,489 entries.
Since v4: +65,711,653 added, 39,324,993 removed, 276,539 changed (in sequence), 175,082,297 unchanged (metadata refresh, relabelled v6). Details 👇
October 21, 2025 at 1:26 PM
Sorry to keep you waiting Max! We got overwhelmed with questions on this release. So we wrote another post to clarify some of these queries here – bsky.app/profile/mits...
Not yet, but we are working on it! We wanted to prioritise downloads from individual entry pages, before we expand towards bulk downloads. BRB.
October 7, 2025 at 8:52 PM
Not yet, but we are working on it! We wanted to prioritise downloads from individual entry pages, before we expand towards bulk downloads. BRB.
Likewise Nico! Looking forward to more developments in the near future!
March 11, 2025 at 9:13 AM
Likewise Nico! Looking forward to more developments in the near future!
This is just the start! I’ll be sharing more on this new feature on AlphaFold DB, cool use-cases, and various other updates.
Have you got an interesting domain example? Did you find a case where TED annotations shine (or break) in our new feature?
Let me know! Follow for more updates! 🔜
🧵(6/6)
Have you got an interesting domain example? Did you find a case where TED annotations shine (or break) in our new feature?
Let me know! Follow for more updates! 🔜
🧵(6/6)
March 4, 2025 at 11:51 AM
This is just the start! I’ll be sharing more on this new feature on AlphaFold DB, cool use-cases, and various other updates.
Have you got an interesting domain example? Did you find a case where TED annotations shine (or break) in our new feature?
Let me know! Follow for more updates! 🔜
🧵(6/6)
Have you got an interesting domain example? Did you find a case where TED annotations shine (or break) in our new feature?
Let me know! Follow for more updates! 🔜
🧵(6/6)
And, of course, TED wouldn’t exist without Prof. David Jones & Prof. Christine Orengo’s groups at UCL, who developed and maintain this incredible resource. Their work made this integration possible! 🏗️
@ucl.ac.uk
🧵(5/6)
@ucl.ac.uk
🧵(5/6)
March 4, 2025 at 11:50 AM
And, of course, TED wouldn’t exist without Prof. David Jones & Prof. Christine Orengo’s groups at UCL, who developed and maintain this incredible resource. Their work made this integration possible! 🏗️
@ucl.ac.uk
🧵(5/6)
@ucl.ac.uk
🧵(5/6)
None of this would have been possible without our amazing team! Huge thanks to our PDBe—their work made TED’s integration both seamless and accessible. 🙌
@pdbeurope.bsky.social
🧵(4/6)
@pdbeurope.bsky.social
🧵(4/6)
March 4, 2025 at 11:49 AM
None of this would have been possible without our amazing team! Huge thanks to our PDBe—their work made TED’s integration both seamless and accessible. 🙌
@pdbeurope.bsky.social
🧵(4/6)
@pdbeurope.bsky.social
🧵(4/6)
One great example? Inosine-5'-monophosphate dehydrogenase (AF-Q9GZH3-F1), where TED highlights a CBS-domain nested inside a split Aldolase class I domain. TED annotations + the interactive PAE plot = a powerful way to explore domain organisation and relationship!
🧵(3/6)
🧵(3/6)
AlphaFold Protein Structure Database
AlphaFold Protein Structure Database
alphafold.ebi.ac.uk
March 4, 2025 at 11:48 AM
One great example? Inosine-5'-monophosphate dehydrogenase (AF-Q9GZH3-F1), where TED highlights a CBS-domain nested inside a split Aldolase class I domain. TED annotations + the interactive PAE plot = a powerful way to explore domain organisation and relationship!
🧵(3/6)
🧵(3/6)
TED (The Encyclopedia of Domains) makes it easier to explore structural domains in AlphaFold-predicted proteins. You can visualise functional units, assess domain organisation with the PAE plot, and explore evolutionary relationships through CATH classifications (@cathgene3d.bsky.social).
🧵(2/6)
🧵(2/6)
March 4, 2025 at 11:47 AM
TED (The Encyclopedia of Domains) makes it easier to explore structural domains in AlphaFold-predicted proteins. You can visualise functional units, assess domain organisation with the PAE plot, and explore evolutionary relationships through CATH classifications (@cathgene3d.bsky.social).
🧵(2/6)
🧵(2/6)
Wow, these are all so incredible! Especially the DNA lego bases! I'd love to learn to do this more. Do you have any tips to get started? I know the main bottleneck for me is I don't have GPU rendering capabilities...
November 24, 2024 at 5:51 PM
Wow, these are all so incredible! Especially the DNA lego bases! I'd love to learn to do this more. Do you have any tips to get started? I know the main bottleneck for me is I don't have GPU rendering capabilities...