Nicola Bordin
@nbordin.bsky.social
Research Fellow in Bioinformatics (Proteins + ML + Function) @ CATH University College London | Mountains, Proteins, Food in that order | MSCA Alumn | Replies to emails!
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Nicola Bordin
@nbordin.bsky.social
· Nov 16
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
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 🧵⤵️
Reposted by Nicola Bordin
We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated.
mrc.tal.net/vx/appcentre...
mrc.tal.net/vx/appcentre...
Quick Check Needed
mrc.tal.net
October 29, 2025 at 9:17 AM
We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated.
mrc.tal.net/vx/appcentre...
mrc.tal.net/vx/appcentre...
Reposted by Nicola Bordin
It was lovely to speak at the CATH 30 symposium, celebrating 30 years of the @cathgene3d.bsky.social protein structure classification database. I was presenting recent work on our new generative protein-family language model: preprint coming soon.
September 18, 2025 at 10:33 AM
It was lovely to speak at the CATH 30 symposium, celebrating 30 years of the @cathgene3d.bsky.social protein structure classification database. I was presenting recent work on our new generative protein-family language model: preprint coming soon.
Packing for our first flight with our kid tomorrow. Wish us luck!
We went from 9kg of checked luggage for 2 months in Thailand to 3 checked suitcases and a pram. Send help!
We went from 9kg of checked luggage for 2 months in Thailand to 3 checked suitcases and a pram. Send help!
August 26, 2025 at 4:35 PM
Packing for our first flight with our kid tomorrow. Wish us luck!
We went from 9kg of checked luggage for 2 months in Thailand to 3 checked suitcases and a pram. Send help!
We went from 9kg of checked luggage for 2 months in Thailand to 3 checked suitcases and a pram. Send help!
Reposted by Nicola Bordin
We have a stellar lineup of speakers!
Christine Orengo
Burkhard Rost
Janet Thornton
David Jones
Gonzalo Parra @gonzaparra.bsky.social
Sameer Velankar
Alex Bateman
Maria Martin
Rob Finn
Gerardo Tauriello
Alexey Murzin
Christine Orengo
Burkhard Rost
Janet Thornton
David Jones
Gonzalo Parra @gonzaparra.bsky.social
Sameer Velankar
Alex Bateman
Maria Martin
Rob Finn
Gerardo Tauriello
Alexey Murzin
August 22, 2025 at 10:45 AM
We have a stellar lineup of speakers!
Christine Orengo
Burkhard Rost
Janet Thornton
David Jones
Gonzalo Parra @gonzaparra.bsky.social
Sameer Velankar
Alex Bateman
Maria Martin
Rob Finn
Gerardo Tauriello
Alexey Murzin
Christine Orengo
Burkhard Rost
Janet Thornton
David Jones
Gonzalo Parra @gonzaparra.bsky.social
Sameer Velankar
Alex Bateman
Maria Martin
Rob Finn
Gerardo Tauriello
Alexey Murzin
Reposted by Nicola Bordin
There will be talks from world leaders in structural bioinfomatics on various themes including pioneering protein language models and key international resources including: PDBe, InterPro, UniProt, MGnify, SWISS-MODEL, FrustraEvo and CATH.
August 22, 2025 at 10:45 AM
There will be talks from world leaders in structural bioinfomatics on various themes including pioneering protein language models and key international resources including: PDBe, InterPro, UniProt, MGnify, SWISS-MODEL, FrustraEvo and CATH.
Reposted by Nicola Bordin
CATH turns 30 years old this year!
We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses.
www.eventbrite.co.uk/e/protein-an...
We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses.
www.eventbrite.co.uk/e/protein-an...
Protein Annotations in the age of AI
A not-for-profit symposium hosted at UCL - more details about speakers and venue below.
www.eventbrite.co.uk
August 22, 2025 at 10:45 AM
CATH turns 30 years old this year!
We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses.
www.eventbrite.co.uk/e/protein-an...
We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses.
www.eventbrite.co.uk/e/protein-an...
Today I became a British citizen! 🇬🇧
August 13, 2025 at 12:18 PM
Today I became a British citizen! 🇬🇧
#ISMBECCB2025 is over! Back to London tomorrow after a science feast, a talk, and a selfie with John Jumper. Not too bad!
July 24, 2025 at 6:53 PM
#ISMBECCB2025 is over! Back to London tomorrow after a science feast, a talk, and a selfie with John Jumper. Not too bad!
Reposted by Nicola Bordin
Today at 2 PM at 3DSIG #ISMBECCB2025, @nbordin.bsky.social presents our joint work on metagenomic-scale clustering and novel domain discovery in predicted structures!
📄 www.biorxiv.org/content/10.1...
Also check out poster:
B-50 lolalign Sensitive structural alignments by Lasse
B-123 BFVD by Rachel
📄 www.biorxiv.org/content/10.1...
Also check out poster:
B-50 lolalign Sensitive structural alignments by Lasse
B-123 BFVD by Rachel
Metagenomic-scale analysis of the predicted protein structure universe
Protein structure prediction breakthroughs, notably AlphaFold2 and ESMfold, have led to an unprecedented influx of computationally derived structures. The AlphaFold Protein Structure Database now prov...
www.biorxiv.org
July 22, 2025 at 9:10 AM
Today at 2 PM at 3DSIG #ISMBECCB2025, @nbordin.bsky.social presents our joint work on metagenomic-scale clustering and novel domain discovery in predicted structures!
📄 www.biorxiv.org/content/10.1...
Also check out poster:
B-50 lolalign Sensitive structural alignments by Lasse
B-123 BFVD by Rachel
📄 www.biorxiv.org/content/10.1...
Also check out poster:
B-50 lolalign Sensitive structural alignments by Lasse
B-123 BFVD by Rachel
July 20, 2025 at 9:09 AM
Reposted by Nicola Bordin
"in 2025 we will have flying cars" 😂😂😂
July 5, 2025 at 4:17 PM
"in 2025 we will have flying cars" 😂😂😂
Exclusive: An international scientific competition widely credited with spurring the development of artificial intelligence for biology appears to be on its deathbed. scim.ag/44ukS90
Exclusive: Famed protein structure competition nears end as NIH grant money runs out
Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold
scim.ag
July 3, 2025 at 9:33 AM
Reposted by Nicola Bordin
We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments.
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...
May 15, 2025 at 2:03 PM
We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments.
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...
Our latest preprint is out on bioRxiv!
A collaboration between the groups of @martinsteinegger.bsky.social , David Jones and Christine Orengo, we clustered AlphaFold Database and ESMatlas, a whopping 821 million proteins!
We reveal biome-specific groups & over 11k novel domain combinations.
A collaboration between the groups of @martinsteinegger.bsky.social , David Jones and Christine Orengo, we clustered AlphaFold Database and ESMatlas, a whopping 821 million proteins!
We reveal biome-specific groups & over 11k novel domain combinations.
Metagenomic-scale analysis of the predicted protein structure universe
Protein structure prediction breakthroughs, notably AlphaFold2 and ESMfold, have led to an unprecedented influx of computationally derived structures. The AlphaFold Protein Structure Database now prov...
www.biorxiv.org
April 28, 2025 at 11:16 AM
Our latest preprint is out on bioRxiv!
A collaboration between the groups of @martinsteinegger.bsky.social , David Jones and Christine Orengo, we clustered AlphaFold Database and ESMatlas, a whopping 821 million proteins!
We reveal biome-specific groups & over 11k novel domain combinations.
A collaboration between the groups of @martinsteinegger.bsky.social , David Jones and Christine Orengo, we clustered AlphaFold Database and ESMatlas, a whopping 821 million proteins!
We reveal biome-specific groups & over 11k novel domain combinations.
I dropped off the radar for a bit, as Aria, our daughter, was born two months earlier than expected!
My wife was discharged from the hospital a week later after being stabilised.
Aria has spent the last 40 days in the Neonatal Unit at Hillingdon Hospital, with wonderful care from the NHS.
My wife was discharged from the hospital a week later after being stabilised.
Aria has spent the last 40 days in the Neonatal Unit at Hillingdon Hospital, with wonderful care from the NHS.
April 9, 2025 at 7:08 PM
I dropped off the radar for a bit, as Aria, our daughter, was born two months earlier than expected!
My wife was discharged from the hospital a week later after being stabilised.
Aria has spent the last 40 days in the Neonatal Unit at Hillingdon Hospital, with wonderful care from the NHS.
My wife was discharged from the hospital a week later after being stabilised.
Aria has spent the last 40 days in the Neonatal Unit at Hillingdon Hospital, with wonderful care from the NHS.
See you in Liverpool at ISMB/ECCB 2025!
March 27, 2025 at 10:52 AM
See you in Liverpool at ISMB/ECCB 2025!
First time sitting on the “attack” end of a PhD viva! Really enjoyed the experience!
March 25, 2025 at 3:02 PM
First time sitting on the “attack” end of a PhD viva! Really enjoyed the experience!
Reposted by Nicola Bordin
AlphaFold DB now has TED integrated! This is a special one for me — my first project where I took ownership from start to finish, bringing together different teams to integrate domain annotations into #AlphaFold DB. A huge learning experience, and I’m excited to finally see it live!
🧵(1/6)
🧵(1/6)
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
March 4, 2025 at 11:46 AM
AlphaFold DB now has TED integrated! This is a special one for me — my first project where I took ownership from start to finish, bringing together different teams to integrate domain annotations into #AlphaFold DB. A huge learning experience, and I’m excited to finally see it live!
🧵(1/6)
🧵(1/6)
Reposted by Nicola Bordin
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
March 3, 2025 at 4:33 PM
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
Reposted by Nicola Bordin
Excited to share PoET-2, our next breakthrough in protein language modeling. It represents a fundamental shift in how AI learns from evolutionary sequences. 🧵 1/13
February 11, 2025 at 2:30 PM
Excited to share PoET-2, our next breakthrough in protein language modeling. It represents a fundamental shift in how AI learns from evolutionary sequences. 🧵 1/13
Just booked flights and accommodation for the ML4NGP symposium followed by 3DBioinfo in Barcelona in March!
Looking forward to see friends and collaborators!
Straight to Italy for sitting on a PhD viva panel, busy weeks!
Looking forward to see friends and collaborators!
Straight to Italy for sitting on a PhD viva panel, busy weeks!
January 22, 2025 at 8:00 PM
Just booked flights and accommodation for the ML4NGP symposium followed by 3DBioinfo in Barcelona in March!
Looking forward to see friends and collaborators!
Straight to Italy for sitting on a PhD viva panel, busy weeks!
Looking forward to see friends and collaborators!
Straight to Italy for sitting on a PhD viva panel, busy weeks!
Reposted by Nicola Bordin
Foldseek 10 with 4-27x (1-8 GPUs) faster search through MMseqs2-GPU. Faster ProstT5 protein search w/o structure prediction through multi-GPU/Apple Metal, new BFVD/BFMD databases and multimer clustering (preview).
💾 github.com/steineggerla...
📄 www.biorxiv.org/content/10.1...
🐍 available in bioconda
💾 github.com/steineggerla...
📄 www.biorxiv.org/content/10.1...
🐍 available in bioconda
January 20, 2025 at 2:56 PM
Foldseek 10 with 4-27x (1-8 GPUs) faster search through MMseqs2-GPU. Faster ProstT5 protein search w/o structure prediction through multi-GPU/Apple Metal, new BFVD/BFMD databases and multimer clustering (preview).
💾 github.com/steineggerla...
📄 www.biorxiv.org/content/10.1...
🐍 available in bioconda
💾 github.com/steineggerla...
📄 www.biorxiv.org/content/10.1...
🐍 available in bioconda
A really good day! Submitted a grant/TT proposal, finished reviewing a PhD thesis and wrapping up the last chapters of Shogun!
January 14, 2025 at 7:15 PM
A really good day! Submitted a grant/TT proposal, finished reviewing a PhD thesis and wrapping up the last chapters of Shogun!
Reposted by Nicola Bordin
We are excited to announce the 1st webinar from this year on January 20th!
This time we will have a full lecture by Prof. David Jones from UCL presenting their recent publication in ScienceMagazine: www.science.org/doi/abs/10.1...
Register here:
elixir-europe.org/events/3d-bi...
This time we will have a full lecture by Prof. David Jones from UCL presenting their recent publication in ScienceMagazine: www.science.org/doi/abs/10.1...
Register here:
elixir-europe.org/events/3d-bi...
January 12, 2025 at 11:45 PM
We are excited to announce the 1st webinar from this year on January 20th!
This time we will have a full lecture by Prof. David Jones from UCL presenting their recent publication in ScienceMagazine: www.science.org/doi/abs/10.1...
Register here:
elixir-europe.org/events/3d-bi...
This time we will have a full lecture by Prof. David Jones from UCL presenting their recent publication in ScienceMagazine: www.science.org/doi/abs/10.1...
Register here:
elixir-europe.org/events/3d-bi...
Closed the accounts on the other place!
January 5, 2025 at 3:54 PM
Closed the accounts on the other place!