September 11, 2023 at 9:12 PM
Predicted structures from the AFDB are poor substitutes for experimental structures when training inverse folding NNs. Here, authors show that this is because they are "too perfect", and passing them through a custom-trained AFDB-to-PDB NN helps fix this
threadreaderapp.com/thread/19384...
threadreaderapp.com/thread/19384...
June 27, 2025 at 11:33 AM
Predicted structures from the AFDB are poor substitutes for experimental structures when training inverse folding NNs. Here, authors show that this is because they are "too perfect", and passing them through a custom-trained AFDB-to-PDB NN helps fix this
threadreaderapp.com/thread/19384...
threadreaderapp.com/thread/19384...
noch jemand hungrig?
bsky.app/profile/robe...
bsky.app/profile/jk-r...
bsky.app/profile/afdb...
bsky.app/profile/obsc...
bsky.app/profile/robe...
bsky.app/profile/jk-r...
bsky.app/profile/afdb...
bsky.app/profile/obsc...
October 28, 2023 at 12:00 PM
BFVD v3 contains 5.8M viral protein structures, 16× more than v2; 75% high quality, filling a major gap in AFDB coverage. It fully covers 72.6% of reference proteomes and spans 72.7% of ICTV species. Great work by @eunbelivable.bsky.social et al.
📄 www.biorxiv.org/content/10.6...
🌐 bfvd.foldseek.com
📄 www.biorxiv.org/content/10.6...
🌐 bfvd.foldseek.com
September 19, 2026 at 6:48 AM
BFVD v3 contains 5.8M viral protein structures, 16× more than v2; 75% high quality, filling a major gap in AFDB coverage. It fully covers 72.6% of reference proteomes and spans 72.7% of ICTV species. Great work by @eunbelivable.bsky.social et al.
📄 www.biorxiv.org/content/10.6...
🌐 bfvd.foldseek.com
📄 www.biorxiv.org/content/10.6...
🌐 bfvd.foldseek.com
Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁
The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities.
This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.
Explore the new datasets in the AlphaFold Database.
www.ebi.ac.uk/about/news/u...
This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.
Explore the new datasets in the AlphaFold Database.
www.ebi.ac.uk/about/news/u...
AlphaFold Database welcomes community datasets
Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities
www.ebi.ac.uk
February 18, 2026 at 4:46 AM
Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁
AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
April 27, 2025 at 12:13 AM
AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
Some updates:
- Remote Multiplayer support fixed.
- Adding support for custom PDB/AFDB inputs! (Initially implemented by @ianandersonlol.bsky.social )
- Remote Multiplayer support fixed.
- Adding support for custom PDB/AFDB inputs! (Initially implemented by @ianandersonlol.bsky.social )
September 15, 2026 at 3:44 PM
Some updates:
- Remote Multiplayer support fixed.
- Adding support for custom PDB/AFDB inputs! (Initially implemented by @ianandersonlol.bsky.social )
- Remote Multiplayer support fixed.
- Adding support for custom PDB/AFDB inputs! (Initially implemented by @ianandersonlol.bsky.social )
From Sameer Velankar & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #AlphaFold #Protein #Structure #Database 2025: a redesigned interface and updated structural coverage | #Bioinformatics #Proteomics #OpenScience #AFDB 🧪🔓 CC/ @ebi.embl.org
⬇️
academic.oup.com/nar/advance-...
⬇️
academic.oup.com/nar/advance-...
AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage
Abstract. The AlphaFold Protein Structure Database (AFDB; https://alphafold.ebi.ac.uk), developed by EMBL–EBI and Google DeepMind, provides open access to
academic.oup.com
November 24, 2025 at 12:56 AM
From Sameer Velankar & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #AlphaFold #Protein #Structure #Database 2025: a redesigned interface and updated structural coverage | #Bioinformatics #Proteomics #OpenScience #AFDB 🧪🔓 CC/ @ebi.embl.org
⬇️
academic.oup.com/nar/advance-...
⬇️
academic.oup.com/nar/advance-...
45 novel protein folds in the updated AFESM (AFDB + ESMatlas) manuscript:
• 12 high-confidence folds in AFESM
• 33 by ColabFold-repredicting 2.3M low-quality domains
We show AFDB captures most domains already and ESMfold struggles with novelty
🌏 afesm.foldseek.com
📄 biorxiv.org/content/10.1...
• 12 high-confidence folds in AFESM
• 33 by ColabFold-repredicting 2.3M low-quality domains
We show AFDB captures most domains already and ESMfold struggles with novelty
🌏 afesm.foldseek.com
📄 biorxiv.org/content/10.1...
AFESM Clusters
Foldseek clustered 820M AlphaFold DB + ESMatlas structures
afesm.foldseek.com
April 3, 2026 at 7:29 AM
45 novel protein folds in the updated AFESM (AFDB + ESMatlas) manuscript:
• 12 high-confidence folds in AFESM
• 33 by ColabFold-repredicting 2.3M low-quality domains
We show AFDB captures most domains already and ESMfold struggles with novelty
🌏 afesm.foldseek.com
📄 biorxiv.org/content/10.1...
• 12 high-confidence folds in AFESM
• 33 by ColabFold-repredicting 2.3M low-quality domains
We show AFDB captures most domains already and ESMfold struggles with novelty
🌏 afesm.foldseek.com
📄 biorxiv.org/content/10.1...
Hi TED! 👋
Out now in Science, we are finally ready to make our classification of all domains in AFDB v4 available to all!
A joint effort of @cathgene3d.bsky.social and the Jones group (PSIPRED), here's a link to the article
www.science.org/doi/10.1126/...
1/6 🧵⤵️
Out now in Science, we are finally ready to make our classification of all domains in AFDB v4 available to all!
A joint effort of @cathgene3d.bsky.social and the Jones group (PSIPRED), here's a link to the article
www.science.org/doi/10.1126/...
1/6 🧵⤵️
Exploring structural diversity across the protein universe with The Encyclopedia of Domains
The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and ...
www.science.org
November 16, 2024 at 2:59 PM
Hi TED! 👋
Out now in Science, we are finally ready to make our classification of all domains in AFDB v4 available to all!
A joint effort of @cathgene3d.bsky.social and the Jones group (PSIPRED), here's a link to the article
www.science.org/doi/10.1126/...
1/6 🧵⤵️
Out now in Science, we are finally ready to make our classification of all domains in AFDB v4 available to all!
A joint effort of @cathgene3d.bsky.social and the Jones group (PSIPRED), here's a link to the article
www.science.org/doi/10.1126/...
1/6 🧵⤵️
Clustering 821M structures (AFDB&ESMatlas) into 5.12M groups reveals biome-specific groups but only 1 new fold (many novel domain combinations though!).
@jingiyeo.bsky.social @yewonhan.bsky.social @nbordin.bsky.social @hbkgenomics.bsky.social @milot.bsky.social @martinsteinegger.bsky.social
@jingiyeo.bsky.social @yewonhan.bsky.social @nbordin.bsky.social @hbkgenomics.bsky.social @milot.bsky.social @martinsteinegger.bsky.social
April 29, 2025 at 2:21 PM
Clustering 821M structures (AFDB&ESMatlas) into 5.12M groups reveals biome-specific groups but only 1 new fold (many novel domain combinations though!).
@jingiyeo.bsky.social @yewonhan.bsky.social @nbordin.bsky.social @hbkgenomics.bsky.social @milot.bsky.social @martinsteinegger.bsky.social
@jingiyeo.bsky.social @yewonhan.bsky.social @nbordin.bsky.social @hbkgenomics.bsky.social @milot.bsky.social @martinsteinegger.bsky.social
Folddisco webserver result view update:
- Added description texts for AFDB
- Integrated TaxoView taxonomy visualization & filter by @sunjaelee.bsky.social
- Inter-residue distance clustering by DBSCAN to explore motif diversity.
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
- Added description texts for AFDB
- Integrated TaxoView taxonomy visualization & filter by @sunjaelee.bsky.social
- Inter-residue distance clustering by DBSCAN to explore motif diversity.
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
July 22, 2025 at 6:11 PM
Folddisco webserver result view update:
- Added description texts for AFDB
- Integrated TaxoView taxonomy visualization & filter by @sunjaelee.bsky.social
- Inter-residue distance clustering by DBSCAN to explore motif diversity.
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
- Added description texts for AFDB
- Integrated TaxoView taxonomy visualization & filter by @sunjaelee.bsky.social
- Inter-residue distance clustering by DBSCAN to explore motif diversity.
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
From viral assemblies to how proteases recognise their substrates: starting points for vaccine and antiviral experiments.
The predictions are open through AFDB, so researchers can use them without repeating the computation: alphafold.ebi.ac.uk
The predictions are open through AFDB, so researchers can use them without repeating the computation: alphafold.ebi.ac.uk
September 24, 2026 at 4:45 PM
From viral assemblies to how proteases recognise their substrates: starting points for vaccine and antiviral experiments.
The predictions are open through AFDB, so researchers can use them without repeating the computation: alphafold.ebi.ac.uk
The predictions are open through AFDB, so researchers can use them without repeating the computation: alphafold.ebi.ac.uk
New video 🎥
The AlphaFold-Multimer prediction for your protein looks great. But how confident should you actually be in it?
Razan Abbara breaks down the 5 confidence metrics behind every AFDB multimer entry:
pLDDT · ipTM · ipSAE · pDockQ2 · LIS 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AFDB
The AlphaFold-Multimer prediction for your protein looks great. But how confident should you actually be in it?
Razan Abbara breaks down the 5 confidence metrics behind every AFDB multimer entry:
pLDDT · ipTM · ipSAE · pDockQ2 · LIS 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AFDB
September 3, 2026 at 12:26 PM
New video 🎥
The AlphaFold-Multimer prediction for your protein looks great. But how confident should you actually be in it?
Razan Abbara breaks down the 5 confidence metrics behind every AFDB multimer entry:
pLDDT · ipTM · ipSAE · pDockQ2 · LIS 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AFDB
The AlphaFold-Multimer prediction for your protein looks great. But how confident should you actually be in it?
Razan Abbara breaks down the 5 confidence metrics behind every AFDB multimer entry:
pLDDT · ipTM · ipSAE · pDockQ2 · LIS 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AFDB
We're hiring a 𝐓𝐫𝐚𝐢𝐧𝐢𝐧𝐠 𝐒𝐩𝐞𝐜𝐢𝐚𝐥𝐢𝐬𝐭 for 𝐀𝐥𝐩𝐡𝐚𝐅𝐨𝐥𝐝 𝐃𝐚𝐭𝐚𝐛𝐚𝐬𝐞 (AFDB)! Join our team to develop training content, create workshops, and drive global engagement with AlphaFold and AFDB.
Full-time, hybrid role.
Apply now! embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
#AFDB #Jobs #emblebi
Full-time, hybrid role.
Apply now! embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
#AFDB #Jobs #emblebi
January 26, 2026 at 10:55 AM
We're hiring a 𝐓𝐫𝐚𝐢𝐧𝐢𝐧𝐠 𝐒𝐩𝐞𝐜𝐢𝐚𝐥𝐢𝐬𝐭 for 𝐀𝐥𝐩𝐡𝐚𝐅𝐨𝐥𝐝 𝐃𝐚𝐭𝐚𝐛𝐚𝐬𝐞 (AFDB)! Join our team to develop training content, create workshops, and drive global engagement with AlphaFold and AFDB.
Full-time, hybrid role.
Apply now! embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
#AFDB #Jobs #emblebi
Full-time, hybrid role.
Apply now! embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
#AFDB #Jobs #emblebi
Ich sag Account "AfD Berlin" und Ihr sagt?
bsky.app/profile/afdb...
bsky.app/profile/afdb...
bsky.app
October 19, 2023 at 5:33 AM
Ich sag Account "AfD Berlin" und Ihr sagt?
bsky.app/profile/afdb...
bsky.app/profile/afdb...
The latest update to the AlphaFold Database (AFDB) is now published in NAR.
The release aligns AFDB with UniProt 2025_03 and introduces a redesigned entry page with integrated annotations, domains, summaries, and a 3D viewer.
📄 Read more: academic.oup.com/nar/advance-...
The release aligns AFDB with UniProt 2025_03 and introduces a redesigned entry page with integrated annotations, domains, summaries, and a 3D viewer.
📄 Read more: academic.oup.com/nar/advance-...
December 4, 2025 at 2:00 PM
The latest update to the AlphaFold Database (AFDB) is now published in NAR.
The release aligns AFDB with UniProt 2025_03 and introduces a redesigned entry page with integrated annotations, domains, summaries, and a 3D viewer.
📄 Read more: academic.oup.com/nar/advance-...
The release aligns AFDB with UniProt 2025_03 and introduces a redesigned entry page with integrated annotations, domains, summaries, and a 3D viewer.
📄 Read more: academic.oup.com/nar/advance-...
AfDB expands Africa development push through Hyundai partnership
#AfricanDevelopmentBank #AfDB #HyundaiMotorGroup #Africa #greenindustrialisation #sustainablemobility #cleanenergy #electricvehicles #criticalminerals
#AfricanDevelopmentBank #AfDB #HyundaiMotorGroup #Africa #greenindustrialisation #sustainablemobility #cleanenergy #electricvehicles #criticalminerals
AfDB expands Africa development push through Hyundai partnership
The planned cooperation covers clean energy, mobility, logistics, electric vehicles, manufacturing and skills, while Morocco has secured €405 million in AfDB financing.
www.logupdateafrica.com
September 18, 2026 at 3:12 PM
AfDB expands Africa development push through Hyundai partnership
#AfricanDevelopmentBank #AfDB #HyundaiMotorGroup #Africa #greenindustrialisation #sustainablemobility #cleanenergy #electricvehicles #criticalminerals
#AfricanDevelopmentBank #AfDB #HyundaiMotorGroup #Africa #greenindustrialisation #sustainablemobility #cleanenergy #electricvehicles #criticalminerals
Fletcher-class destroyer USS Claxton (DD-571): Kamikaze suicide attack off Leyte, 1/11.1944.
Baltimore-class cruiser USS Canberra (CA-70): Hit by an aerial torpedo off Leyte, 13/10.1944.
Fletcher-class destroyer USS Killen (DD-593): Kamikaze suicide attack off Leyte, 1/11.1944.
#NavalHistory
Baltimore-class cruiser USS Canberra (CA-70): Hit by an aerial torpedo off Leyte, 13/10.1944.
Fletcher-class destroyer USS Killen (DD-593): Kamikaze suicide attack off Leyte, 1/11.1944.
#NavalHistory
USS AFDB-2 - Wikipedia
en.wikipedia.org
September 24, 2026 at 9:50 PM
Fletcher-class destroyer USS Claxton (DD-571): Kamikaze suicide attack off Leyte, 1/11.1944.
Baltimore-class cruiser USS Canberra (CA-70): Hit by an aerial torpedo off Leyte, 13/10.1944.
Fletcher-class destroyer USS Killen (DD-593): Kamikaze suicide attack off Leyte, 1/11.1944.
#NavalHistory
Baltimore-class cruiser USS Canberra (CA-70): Hit by an aerial torpedo off Leyte, 13/10.1944.
Fletcher-class destroyer USS Killen (DD-593): Kamikaze suicide attack off Leyte, 1/11.1944.
#NavalHistory
Adding support for interactive MSA viewing, including coloring by entropy! Auto download from AFDB (for both uniprot and pdb entries). (4/4)
November 19, 2025 at 8:15 AM
Adding support for interactive MSA viewing, including coloring by entropy! Auto download from AFDB (for both uniprot and pdb entries). (4/4)
Now AFDB allows exploration of viral structures🦠
The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities.
This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.
Explore the new datasets in the AlphaFold Database.
www.ebi.ac.uk/about/news/u...
This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.
Explore the new datasets in the AlphaFold Database.
www.ebi.ac.uk/about/news/u...
AlphaFold Database welcomes community datasets
Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities
www.ebi.ac.uk
February 17, 2026 at 2:17 PM
Now AFDB allows exploration of viral structures🦠
Good lord, the FoldSeek clustering of all AlphaFold structures is incredible. Just stunning. Vastly expands the taxonomic breadth of microbes that encode homologous structures that we care about. Paper here: www.nature.com/articles/s41... and website to search here: cluster.foldseek.com
AFDB Clusters
cluster.foldseek.com
September 13, 2023 at 7:43 PM
Good lord, the FoldSeek clustering of all AlphaFold structures is incredible. Just stunning. Vastly expands the taxonomic breadth of microbes that encode homologous structures that we care about. Paper here: www.nature.com/articles/s41... and website to search here: cluster.foldseek.com
AfDB raises $11 billion for low-cost lending window, no word on US funding reut.rs/4qxLBuP
AfDB raises $11 billion for low-cost lending window, no word on US funding
The African Development Bank (AfDB) raised $11 billion for its fund that lends money to low-income countries on favourable terms, it said on Tuesday, surpassing the previous replenishment round's figure but falling short of its initial target.
reut.rs
December 17, 2025 at 12:05 AM
AfDB raises $11 billion for low-cost lending window, no word on US funding reut.rs/4qxLBuP