Author | Lightnews

Paulyna Magaña @paulynamagana.bsky.social · 14d

Check out this thread for more information about the AFDV v6 release 👇🏽

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 15d

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 👇

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Paulyna Magaña @paulynamagana.bsky.social · 14d

Your direct links to structures have a new format.

Old: alphafold.com/entry/P40763
New: alphafold.com/entry/AF-P40...

Simply add 'AF-' and '-F1' to the UniProt ID. Update your bookmarks and code!

AlphaFold Protein Structure Database

alphafold.com

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Paulyna Magaña @paulynamagana.bsky.social · 14d

AlphaFold DB v6 is here! 🚀
Heads up on key updates:
🔹 Website now only serves v6
🔹 New URL format!!
🔹 Dual API active for 9 months (retirement: 25-06-2026)

Use the AlphaFold API for reliable access. Time to update those bookmarks & scripts!

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 29d

📣Important update for #AlphaFold API users! New API fields launched on October 7th, 2025. We’ll maintain BOTH fields until June 25, 2026! Check the docs! 🔗
For more information, read the news item: www.ebi.ac.uk/pdbe/news/br...

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Paulyna Magaña @paulynamagana.bsky.social · Jan 16

Teamed up with Google Deepmind & @training.ebi.embl.org to launch the AlphaFold Education Summit!
We're helping researchers master AlphaFold & analyse macromolecular structures, driving impactful, responsible use of the system & database

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Paulyna Magaña @paulynamagana.bsky.social · Jan 13

15,319 new structures were added to the PDB archive in 2024! Most X-ray structures fell within the 1-2.5 Å range, with 49 structures exceeding 1 Å resolution! The best resolution? An astounding 0.70 Å for Crambin (PDBe.org/9ewk)

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Reposted by Paulyna Magaña

Boston Protein Design and Modeling Club @bpdmc.org · Dec 11

See you tonight at @harvardmed.bsky.social for an amazing seminar by Mireia to cap off 2024!

*Please note the change of location*

Boston Protein Design and Modeling Club @bpdmc.org · Nov 22

There's just one meeting left in 2024, and we have a spectacular seminar by Mireia Solà Colom lined up for you! Join us at 7pm in Room 181, Building 68, MIT on Wednesday, December 11th.

"De novo design of miniprotein-based natural killer cell engagers"

See you there & Happy Thanksgiving!
bpdmc.org

schedule

introduction and membership Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...

bpdmc.org

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Paulyna Magaña @paulynamagana.bsky.social · Nov 27

Was playing around with #AlphaFold Server and saw the example JSON for DNA sequence is "GATTACA". Either someone at Google DeepMind is a huge sci-fi nerd (like me!), or they're trying to tell us something about the future of genetic engineering... 🤔😜

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Paulyna Magaña @paulynamagana.bsky.social · Nov 26

Me: spends 3 hours making a presentation

Also me: spends 2 hours looking for the perfect font to use on the title slide 💀💀💀

Anyone else get ridiculously obsessed with tiny details that probably no one else even notices? Asking for a friend... 😅

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Reposted by Paulyna Magaña

Magnus Kjærgaard @proteinmagnus.bsky.social · Nov 25

Do you need a starting pack of researcher working on intrinsically disordered proteins?

Well, you might head over to @idpseminars.bsky.social and hit followers.

Tw***** was important for the birth of IDPseminars and for spreading the word. It would be cool to re-kindle that community here.

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Reposted by Paulyna Magaña

EMBL-EBI @ebi.embl.org · Nov 21

Introducing the first comprehensive spatial atlas of the developing human thymus.

Find out more and how our researchers helped to develop a new high resolution spatial mapping method to study the stages of thymus development.

🖥️🧬🧪

www.ebi.ac.uk/about/news/a...

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Paulyna Magaña @paulynamagana.bsky.social · Nov 24

The BFVD just leveled up!🔥 MSAs and conservation scores are now available alongside their massive collection of 351k+ viral protein structures! Great news @milot.bsky.social!! 🎉

Milot Mirdita @milot.bsky.social · Nov 24

One more freshly baked BFVD website feature:
Download the Multiple Sequence Alignments used to predict the structures or visualize MSA conservation directly in the webserver.
🖥️ bfvd.foldseek.com 🧬🧶

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Reposted by Paulyna Magaña

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Nov 23

Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web.
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...

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Paulyna Magaña @paulynamagana.bsky.social · Nov 21

Hey Bluesky folks! Make sure you're following pdbeurope.bsky.social for all the latest updates on the #AlphaFold Database!

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Reposted by Paulyna Magaña

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Jan 5

As we head into 2024, let's take one final look back at 2023 and how the year unfolded in the PDB archive. There were 14488 entries released last year but what more can we find out about those structures ⚖️? A thread 1/10 🧵

wwPDB letters spelled-out with protein structures

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Paulyna Magaña @paulynamagana.bsky.social · Jan 3

Don't miss @sganguly.bsky.social & @glevans.bsky.social bringing the latest insights on wwPDB & PDBe to the CCP4 Summer Weekend! Join their Lunchtime Bytes session on Day 3 (Jan 5th). It's going to be a protein-packed lunch break! #CCP4SW 2024

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Jan 3

Excited to be attending 🔷 #CCP4SW 2024 / @ccp4_mx Study Weekend 🔷. In-person Lunchtime Bytes session on Day3 (Jan 5th) with PDBe. Look out for friendly PDBe representatives Sue (@sganguly) & Gen (@gleevans).

Conference lobby with CCP4 conference advertised

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Reposted by Paulyna Magaña

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Jan 3

Excited to be attending 🔷 #CCP4SW 2024 / @ccp4_mx Study Weekend 🔷. In-person Lunchtime Bytes session on Day3 (Jan 5th) with PDBe. Look out for friendly PDBe representatives Sue (@sganguly) & Gen (@gleevans).

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