Paulyna Magaña
@paulynamagana.bsky.social
Building bridges in the protein world 👩🏻💻
Bioinformatician at AlphaFold Database (part of PDBe)
Bioinformatician at AlphaFold Database (part of PDBe)
Check out this thread for more information about the AFDV v6 release 👇🏽
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 22, 2025 at 5:48 PM
Check out this thread for more information about the AFDV v6 release 👇🏽
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!
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!
📣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...
For more information, read the news item: www.ebi.ac.uk/pdbe/news/br...
October 22, 2025 at 5:39 PM
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!
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!
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
We're helping researchers master AlphaFold & analyse macromolecular structures, driving impactful, responsible use of the system & database
January 16, 2025 at 5:56 PM
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
We're helping researchers master AlphaFold & analyse macromolecular structures, driving impactful, responsible use of the system & database
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)
January 13, 2025 at 11:06 PM
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)
Reposted by Paulyna Magaña
See you tonight at @harvardmed.bsky.social for an amazing seminar by Mireia to cap off 2024!
*Please note the change of location*
*Please note the change of location*
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
"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
December 11, 2024 at 11:57 AM
See you tonight at @harvardmed.bsky.social for an amazing seminar by Mireia to cap off 2024!
*Please note the change of location*
*Please note the change of location*
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... 🤔😜
November 27, 2024 at 5:46 PM
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... 🤔😜
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... 😅
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... 😅
November 26, 2024 at 1:31 PM
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... 😅
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... 😅
Reposted by Paulyna Magaña
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.
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.
November 25, 2024 at 11:44 AM
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.
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.
Reposted by Paulyna Magaña
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...
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...
November 21, 2024 at 11:14 AM
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...
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...
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!! 🎉
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 🧬🧶
Download the Multiple Sequence Alignments used to predict the structures or visualize MSA conservation directly in the webserver.
🖥️ bfvd.foldseek.com 🧬🧶
November 24, 2024 at 6:00 PM
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!! 🎉
Reposted by Paulyna Magaña
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-...
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...
November 23, 2024 at 9:12 PM
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-...
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...
Hey Bluesky folks! Make sure you're following pdbeurope.bsky.social for all the latest updates on the #AlphaFold Database!
November 21, 2024 at 11:53 AM
Hey Bluesky folks! Make sure you're following pdbeurope.bsky.social for all the latest updates on the #AlphaFold Database!
Reposted by Paulyna Magaña
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 🧵
January 5, 2024 at 5:46 PM
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 🧵
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
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).
January 3, 2024 at 4:10 PM
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
Reposted by Paulyna Magaña
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).
January 3, 2024 at 2:19 PM
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).