August 22, 2025 at 12:20 PM
Amazing talk by @martinsteinegger.bsky.social at the #StructuralPhylogenetics meeting in Brisbane @strphy.bsky.social
The meeting is going to be live for the next 2 days. Excited to see what happens next. #Evolution
The meeting is going to be live for the next 2 days. Excited to see what happens next. #Evolution
February 16, 2026 at 5:47 AM
Amazing talk by @martinsteinegger.bsky.social at the #StructuralPhylogenetics meeting in Brisbane @strphy.bsky.social
The meeting is going to be live for the next 2 days. Excited to see what happens next. #Evolution
The meeting is going to be live for the next 2 days. Excited to see what happens next. #Evolution
Talking about structure-based protein annotations in weid critters (or „Why we shouldn’t say ‘structural homolog’!”). Thanks for having me @strphy.bsky.social #StrPhy #StrPhy26 #StructuralPhylogenetics
February 16, 2026 at 11:50 PM
Talking about structure-based protein annotations in weid critters (or „Why we shouldn’t say ‘structural homolog’!”). Thanks for having me @strphy.bsky.social #StrPhy #StrPhy26 #StructuralPhylogenetics
New work: Our earlier work showed that Foldseek characters could be adapted for phylogenetic alignment, treating each character as an evolutionary state. That part holds but there's a hidden assumption baked in that needed unpacking. So lets do that.🧵
#StructuralPhylogenetics #Evolution #Protein
#StructuralPhylogenetics #Evolution #Protein
May 10, 2026 at 5:32 AM
New work: Our earlier work showed that Foldseek characters could be adapted for phylogenetic alignment, treating each character as an evolutionary state. That part holds but there's a hidden assumption baked in that needed unpacking. So lets do that.🧵
#StructuralPhylogenetics #Evolution #Protein
#StructuralPhylogenetics #Evolution #Protein
Protein structure is more conserved than sequence. Work in 2020 (MBE: academic.oup.com/mbe/article/...), showed 3D data unlocks deeper evolutionary signals. A thought was why not go higher than 3D? 🧵
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
February 7, 2026 at 2:53 AM
Protein structure is more conserved than sequence. Work in 2020 (MBE: academic.oup.com/mbe/article/...), showed 3D data unlocks deeper evolutionary signals. A thought was why not go higher than 3D? 🧵
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
The program is now live. An excellent global lineup of speakers - AUS, NZ, Korea, India, Laos, UK, Switzerland, France, Finland, Germany, Hungary, Japan, Uruguay, Mexico and USA. Browse abstracts. Just 3 weeks left. Super excited.
#StrPhy26 #Science #Evolution #StrPhy #StructuralPhylogenetics
#StrPhy26 #Science #Evolution #StrPhy #StructuralPhylogenetics
The program for the SMBE Australasian Protein Structural Phylogenetics Meeting 2026 is now out! Abstract book coming soon.
@official-smbe.bsky.social @proteinmechanic.bsky.social
biosig.lab.uq.edu.au/strphy26/pro...
@official-smbe.bsky.social @proteinmechanic.bsky.social
biosig.lab.uq.edu.au/strphy26/pro...
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
January 26, 2026 at 9:36 AM
The program is now live. An excellent global lineup of speakers - AUS, NZ, Korea, India, Laos, UK, Switzerland, France, Finland, Germany, Hungary, Japan, Uruguay, Mexico and USA. Browse abstracts. Just 3 weeks left. Super excited.
#StrPhy26 #Science #Evolution #StrPhy #StructuralPhylogenetics
#StrPhy26 #Science #Evolution #StrPhy #StructuralPhylogenetics
Wrapping up an incredible final day at the APSPM meeting! Huge thanks to the organizers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social Jordan Douglas and all the speakers for the brilliant talks and rich discussions. Beautiful Brisbane!
#StrPhy #StrPhy26 #StructuralPhylogenetics
#StrPhy #StrPhy26 #StructuralPhylogenetics
February 18, 2026 at 11:50 AM
Wrapping up an incredible final day at the APSPM meeting! Huge thanks to the organizers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social Jordan Douglas and all the speakers for the brilliant talks and rich discussions. Beautiful Brisbane!
#StrPhy #StrPhy26 #StructuralPhylogenetics
#StrPhy #StrPhy26 #StructuralPhylogenetics
We’ve set up a dedicated Bluesky space for structural phylogenetics: @strphy.bsky.social. Follow for community updates.
#StrPhy #StructuralPhylogenetics
#StrPhy #StructuralPhylogenetics
October 9, 2025 at 4:04 AM
We’ve set up a dedicated Bluesky space for structural phylogenetics: @strphy.bsky.social. Follow for community updates.
#StrPhy #StructuralPhylogenetics
#StrPhy #StructuralPhylogenetics
Looking forward to working together in the future and further develop #StructuralPhylogenetics in viruses @spyroslytras.bsky.social
#StrPhy26 #StrPhy
#StrPhy26 #StrPhy
What a great conference!! Leaving Brisbane inspired about the future of structural phylogenetics!
Thanks again to the organisers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and Jordan Douglas for an amazing work putting it all together!
Thanks again to the organisers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and Jordan Douglas for an amazing work putting it all together!
February 20, 2026 at 7:16 PM
Looking forward to working together in the future and further develop #StructuralPhylogenetics in viruses @spyroslytras.bsky.social
#StrPhy26 #StrPhy
#StrPhy26 #StrPhy
Attending a fascinating talk by
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
October 15, 2025 at 2:05 AM
Attending a fascinating talk by
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
#structuralphylogenetics #strphylo #proteins #evolution
Great example of what protein 3D structures can tell us about evolution and the origin of eukaryotes
Great example of what protein 3D structures can tell us about evolution and the origin of eukaryotes
🧵In collaboration with Caroline Puente-Lelievre, Ed Moody, Rosie Cater, and Tom Williams we just submitted a new paper describing the prokaryotic origins of the COMMD protein family. @cpuentelelievre.bsky.social, @rosemaryjcater.bsky.social. @kmichie.bsky.social. 1/n
The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking
The ten eukaryotic COMMD proteins are core components of the Commander complex, with central roles in endosomal membrane trafficking and signalling. Each protein has an α-helical N-terminal (HN) domai...
www.biorxiv.org
September 3, 2025 at 1:44 AM
#structuralphylogenetics #strphylo #proteins #evolution
Great example of what protein 3D structures can tell us about evolution and the origin of eukaryotes
Great example of what protein 3D structures can tell us about evolution and the origin of eukaryotes
New in the #StructuralPhylogenetics special section:
Dixson et al. show that structural and physicochemical features of proteins uncover remote evolutionary relationships and provide a new toolset to revisit mitochondrial enzyme evolution.
@genomebiolevol.bsky.social
Dixson et al. show that structural and physicochemical features of proteins uncover remote evolutionary relationships and provide a new toolset to revisit mitochondrial enzyme evolution.
@genomebiolevol.bsky.social
Inference of Cytochrome P450 Evolutionary History Using Structural and Physicochemical Metrics
Abstract. Cytochrome P450s are a superfamily of heme-binding monooxygenases involved with the detoxification of intrinsic and extrinsic toxins. They are ne
academic.oup.com
October 15, 2025 at 10:52 PM
New in the #StructuralPhylogenetics special section:
Dixson et al. show that structural and physicochemical features of proteins uncover remote evolutionary relationships and provide a new toolset to revisit mitochondrial enzyme evolution.
@genomebiolevol.bsky.social
Dixson et al. show that structural and physicochemical features of proteins uncover remote evolutionary relationships and provide a new toolset to revisit mitochondrial enzyme evolution.
@genomebiolevol.bsky.social
Both alphabets have genuine strengths and large-scale validation lies ahead for both. But conformational noise needs to be measured and accounted for before any structural alphabet can fulfil its phylogenetic potential. Collaborations, Feedback and thoughts are welcome.
#StructuralPhylogenetics
#StructuralPhylogenetics
May 10, 2026 at 5:54 AM
Both alphabets have genuine strengths and large-scale validation lies ahead for both. But conformational noise needs to be measured and accounted for before any structural alphabet can fulfil its phylogenetic potential. Collaborations, Feedback and thoughts are welcome.
#StructuralPhylogenetics
#StructuralPhylogenetics
Structome-TM preprint now live @ www.biorxiv.org/content/10.1...
@biorxivpreprint.bsky.social
#Science #Structome #StructuralPhylogenetics
@biorxivpreprint.bsky.social
#Science #Structome #StructuralPhylogenetics
Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases
The increasing availability of protein structures presents new opportunities for detecting homologous proteins. While global alignment methods are widely used and generally effective, they often strug...
www.biorxiv.org
February 8, 2025 at 9:10 PM
Structome-TM preprint now live @ www.biorxiv.org/content/10.1...
@biorxivpreprint.bsky.social
#Science #Structome #StructuralPhylogenetics
@biorxivpreprint.bsky.social
#Science #Structome #StructuralPhylogenetics
Looking forward to sharing this method as a hands-on workshop in the upcoming meeting
For a full list of workshop we have: biosig.lab.uq.edu.au/strphy26/wor...
#StrPhy26 #StrPhy #StructuralPhylogenetics #Evolution #Brisbane
For a full list of workshop we have: biosig.lab.uq.edu.au/strphy26/wor...
#StrPhy26 #StrPhy #StructuralPhylogenetics #Evolution #Brisbane
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
February 7, 2026 at 3:10 AM
Looking forward to sharing this method as a hands-on workshop in the upcoming meeting
For a full list of workshop we have: biosig.lab.uq.edu.au/strphy26/wor...
#StrPhy26 #StrPhy #StructuralPhylogenetics #Evolution #Brisbane
For a full list of workshop we have: biosig.lab.uq.edu.au/strphy26/wor...
#StrPhy26 #StrPhy #StructuralPhylogenetics #Evolution #Brisbane
Sequence-derived structural alphabets like TEA (www.biorxiv.org/content/10.1...), built from embeddings rather than atomic coordinates, are anchored to the invariant amino acid sequence. Conformational noise is absent by design.
#ProteinLanguageModels #ESM2 #StructuralPhylogenetics
#ProteinLanguageModels #ESM2 #StructuralPhylogenetics
May 10, 2026 at 5:48 AM
Sequence-derived structural alphabets like TEA (www.biorxiv.org/content/10.1...), built from embeddings rather than atomic coordinates, are anchored to the invariant amino acid sequence. Conformational noise is absent by design.
#ProteinLanguageModels #ESM2 #StructuralPhylogenetics
#ProteinLanguageModels #ESM2 #StructuralPhylogenetics
When you change an amino acid, that's an evolutionary event. When a 3Di character changes, is that evolution? Or is it the protein just... moving?
That question is at the heart of our new paper.
👇
www.biorxiv.org/content/10.6...
#StructuralPhylogenetics #MolecularEvolution
That question is at the heart of our new paper.
👇
www.biorxiv.org/content/10.6...
#StructuralPhylogenetics #MolecularEvolution
May 10, 2026 at 5:35 AM
When you change an amino acid, that's an evolutionary event. When a 3Di character changes, is that evolution? Or is it the protein just... moving?
That question is at the heart of our new paper.
👇
www.biorxiv.org/content/10.6...
#StructuralPhylogenetics #MolecularEvolution
That question is at the heart of our new paper.
👇
www.biorxiv.org/content/10.6...
#StructuralPhylogenetics #MolecularEvolution
Distance-based #StructuralPhylogenetics is a powerful approach for exploring deep evolutionary relationships. Tools like those in the #Structome suite make this accessible in web workflows — but there's always been a critical missing piece: confidence estimates for the inferred trees.
#StrPhy (1/3)
#StrPhy (1/3)
March 26, 2026 at 2:21 PM
Distance-based #StructuralPhylogenetics is a powerful approach for exploring deep evolutionary relationships. Tools like those in the #Structome suite make this accessible in web workflows — but there's always been a critical missing piece: confidence estimates for the inferred trees.
#StrPhy (1/3)
#StrPhy (1/3)
Like with the MBE work, DeepRoots introduces a new and much faster way to bootstrap. It achieves this by introducing "Embedding Jitter"—injecting Gaussian noise into the latent space to estimate branch support.
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
February 7, 2026 at 2:56 AM
Like with the MBE work, DeepRoots introduces a new and much faster way to bootstrap. It achieves this by introducing "Embedding Jitter"—injecting Gaussian noise into the latent space to estimate branch support.
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
The logic behind this is #EmergentLatentBiology #ELB & is now formalized in our new paper in Curr Op in #StructuralBiology arguing that transformers organize biophysics into a "substrate" where biology becomes easily-decodable. www.sciencedirect.com/science/arti...
#Strphy #StructuralPhylogenetics
#Strphy #StructuralPhylogenetics
February 7, 2026 at 2:55 AM
The logic behind this is #EmergentLatentBiology #ELB & is now formalized in our new paper in Curr Op in #StructuralBiology arguing that transformers organize biophysics into a "substrate" where biology becomes easily-decodable. www.sciencedirect.com/science/arti...
#Strphy #StructuralPhylogenetics
#Strphy #StructuralPhylogenetics
Enter Structome-DeepRoots which uses high-dimensional embeddings from protein language models to see evolutionary "roots" invisible to geometry alone. It was turned into a web app (still has a lot of bugs 😅). 🔗 biosig.lab.uq.edu.au/structome_de...
#StructuralBiology #StructuralPhylogenetics #StrPhy
#StructuralBiology #StructuralPhylogenetics #StrPhy
Structome-DeepRoots
Structome-DeepRoots: A web server for phylogenetic inference using a novel, high-dimensional structural embedding method.
biosig.lab.uq.edu.au
February 7, 2026 at 2:54 AM
Enter Structome-DeepRoots which uses high-dimensional embeddings from protein language models to see evolutionary "roots" invisible to geometry alone. It was turned into a web app (still has a lot of bugs 😅). 🔗 biosig.lab.uq.edu.au/structome_de...
#StructuralBiology #StructuralPhylogenetics #StrPhy
#StructuralBiology #StructuralPhylogenetics #StrPhy