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
Take two structures of the same protein. Which do you use for phylogenetics? We used 3,749 single-chain NMR ensembles from the PDB to test this. The same protein. Different NMR model. Different 3Di string. We built a web app around this Try it: biosig.lab.uq.edu.au/noisyalphabet
#Structome
#Structome
NoisyAlphabet — Structome
Quantify conformational noise in 3Di structural alphabet encodings from NMR ensembles.
biosig.lab.uq.edu.au
May 10, 2026 at 5:39 AM
Take two structures of the same protein. Which do you use for phylogenetics? We used 3,749 single-chain NMR ensembles from the PDB to test this. The same protein. Different NMR model. Different 3Di string. We built a web app around this Try it: biosig.lab.uq.edu.au/noisyalphabet
#Structome
#Structome
An interesting way to look at encoded structural characters to build alignments and trees downstream. This takes structural phylogenetics one step further in the post-AlphaFold era.
#Evolution #Science #StrPhy
On Confidence Assessment in Structure-Aware Alignments
doi.org/10.1093/gbe/...
#Evolution #Science #StrPhy
On Confidence Assessment in Structure-Aware Alignments
doi.org/10.1093/gbe/...
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments
Abstract. Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-base
doi.org
January 14, 2026 at 11:07 AM
An interesting way to look at encoded structural characters to build alignments and trees downstream. This takes structural phylogenetics one step further in the post-AlphaFold era.
#Evolution #Science #StrPhy
On Confidence Assessment in Structure-Aware Alignments
doi.org/10.1093/gbe/...
#Evolution #Science #StrPhy
On Confidence Assessment in Structure-Aware Alignments
doi.org/10.1093/gbe/...
@proteinmechanic.bsky.social et al. present the web-based Structome-AlignViewer for evaluating structure-aware alignments through spatial mapping of alignment columns to protein structures, and quantitative confidence scoring.
🔗 doi.org/10.1093/gbe/evag004
#genome #evolution #compbio
🔗 doi.org/10.1093/gbe/evag004
#genome #evolution #compbio
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments
Abstract. Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-base
doi.org
January 30, 2026 at 3:45 PM
@proteinmechanic.bsky.social et al. present the web-based Structome-AlignViewer for evaluating structure-aware alignments through spatial mapping of alignment columns to protein structures, and quantitative confidence scoring.
🔗 doi.org/10.1093/gbe/evag004
#genome #evolution #compbio
🔗 doi.org/10.1093/gbe/evag004
#genome #evolution #compbio
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments https://www.biorxiv.org/content/10.1101/2025.05.31.657027v1
June 3, 2025 at 11:49 PM
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments https://www.biorxiv.org/content/10.1101/2025.05.31.657027v1
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments https://www.biorxiv.org/content/10.1101/2025.05.31.657027v1
June 3, 2025 at 11:49 PM
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments https://www.biorxiv.org/content/10.1101/2025.05.31.657027v1
Subsequent work led to Structome-TM! Using the TM-score, it picks on local structural similarity, offering complementarity to explore evolutionary relationships. Together, these tools offer a robust framework for structure-based #phylogenetics. App available here biosig.lab.uq.edu.au/structome_tm/
Structome-TM
Structome-TM: This resource complements Structome-Q in gathering protein structures and distance-based phylogenetic tree reconstruction.
biosig.lab.uq.edu.au
January 22, 2025 at 8:40 AM
Subsequent work led to Structome-TM! Using the TM-score, it picks on local structural similarity, offering complementarity to explore evolutionary relationships. Together, these tools offer a robust framework for structure-based #phylogenetics. App available here biosig.lab.uq.edu.au/structome_tm/
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments https://pubmed.ncbi.nlm.nih.gov/41527918/
January 14, 2026 at 6:48 AM
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments https://pubmed.ncbi.nlm.nih.gov/41527918/
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
Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases https://www.biorxiv.org/content/10.1101/2025.02.08.637224v1
February 8, 2025 at 6:47 PM
Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases https://www.biorxiv.org/content/10.1101/2025.02.08.637224v1
Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases https://www.biorxiv.org/content/10.1101/2025.02.08.637224v1
February 8, 2025 at 6:47 PM
Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases https://www.biorxiv.org/content/10.1101/2025.02.08.637224v1
If you do deep evolutionary analysis - structure-aware characters can help. To ensure correct alignments - give it a try: biosig.lab.uq.edu.au/structome_al...
If you would like any features added, drop a message and will give it a shot.
#Science #Evolution #MolecularEvolution #DeepEvolution
If you would like any features added, drop a message and will give it a shot.
#Science #Evolution #MolecularEvolution #DeepEvolution
June 4, 2025 at 12:31 AM
If you do deep evolutionary analysis - structure-aware characters can help. To ensure correct alignments - give it a try: biosig.lab.uq.edu.au/structome_al...
If you would like any features added, drop a message and will give it a shot.
#Science #Evolution #MolecularEvolution #DeepEvolution
If you would like any features added, drop a message and will give it a shot.
#Science #Evolution #MolecularEvolution #DeepEvolution
🧬 Explore the latest from Bioinformatics Advances: "Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases"
Full article available: https://doi.org/10.1093/bioadv/vbag035
Full article available: https://doi.org/10.1093/bioadv/vbag035
March 2, 2026 at 11:02 AM
🧬 Explore the latest from Bioinformatics Advances: "Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases"
Full article available: https://doi.org/10.1093/bioadv/vbag035
Full article available: https://doi.org/10.1093/bioadv/vbag035
🧵: It's out. Structome-AlignViewer, a web-based resource for evaluating protein structure-aware sequence alignments. It maps alignment columns directly onto structures and helps identify conserved regions. Feedback encouraged. www.biorxiv.org/content/10.1...
#Evolution #MolecularEvolution #Science
#Evolution #MolecularEvolution #Science
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments
Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-based approaches. Encoding three-dimensional protein struct...
www.biorxiv.org
June 4, 2025 at 12:10 AM
🧵: It's out. Structome-AlignViewer, a web-based resource for evaluating protein structure-aware sequence alignments. It maps alignment columns directly onto structures and helps identify conserved regions. Feedback encouraged. www.biorxiv.org/content/10.1...
#Evolution #MolecularEvolution #Science
#Evolution #MolecularEvolution #Science
Explore it here: biosig.lab.uq.edu.au/structome_al...
Free to use, no login required.
Feedback welcome — especially if you're working on deep evolutionary comparisons.
🕰️ Let these structure-aware sequence alignments reveal a distant past that amino acid sequences alone couldn’t reach.
Free to use, no login required.
Feedback welcome — especially if you're working on deep evolutionary comparisons.
🕰️ Let these structure-aware sequence alignments reveal a distant past that amino acid sequences alone couldn’t reach.
Structome-AlignViewer
Structome-AlignViewer is a tool to assess the quality of structural alignments using 3Di character encoding. It provides interactive visualization, confidence scoring, and downloadable full/trimmed al...
biosig.lab.uq.edu.au
June 4, 2025 at 12:26 AM
Explore it here: biosig.lab.uq.edu.au/structome_al...
Free to use, no login required.
Feedback welcome — especially if you're working on deep evolutionary comparisons.
🕰️ Let these structure-aware sequence alignments reveal a distant past that amino acid sequences alone couldn’t reach.
Free to use, no login required.
Feedback welcome — especially if you're working on deep evolutionary comparisons.
🕰️ Let these structure-aware sequence alignments reveal a distant past that amino acid sequences alone couldn’t reach.
Interested in knowing more about distance-based #phylogenetics? Check out #Structome Playground — a no-code interactive educational resource for exploring distance matrices, neighbour-joining trees, and now the resolution limit in real time.
biosig.lab.uq.edu.au/structome_pl...
#StrPhy (3/3)
biosig.lab.uq.edu.au/structome_pl...
#StrPhy (3/3)
Structome-Playground: Learning Structural Phylogenetics
An interactive lab for understanding how geometric noise affects phylogenetic trees. Master the concepts of distance-based calibration and the Duplicate Monophyly Criterion.
biosig.lab.uq.edu.au
March 26, 2026 at 2:30 PM
Interested in knowing more about distance-based #phylogenetics? Check out #Structome Playground — a no-code interactive educational resource for exploring distance matrices, neighbour-joining trees, and now the resolution limit in real time.
biosig.lab.uq.edu.au/structome_pl...
#StrPhy (3/3)
biosig.lab.uq.edu.au/structome_pl...
#StrPhy (3/3)
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
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
But structure-aware alignments can mislead if divergent folds cause misalignments. That’s where Structome-AlignViewer comes in — it helps you evaluate how reliable each alignment column is, and where structural consistency holds up.
June 4, 2025 at 12:21 AM
But structure-aware alignments can mislead if divergent folds cause misalignments. That’s where Structome-AlignViewer comes in — it helps you evaluate how reliable each alignment column is, and where structural consistency holds up.
Future work 1) inclusion of custom structure search 2) and I am working on digesting large scale text data via LLMs to offer meaningful text-based insights per query.
Feedback requested:
What would you improve?
#Structome #StructuralPhylogenetics #Science
Feedback requested:
What would you improve?
#Structome #StructuralPhylogenetics #Science
February 8, 2025 at 9:19 PM
Future work 1) inclusion of custom structure search 2) and I am working on digesting large scale text data via LLMs to offer meaningful text-based insights per query.
Feedback requested:
What would you improve?
#Structome #StructuralPhylogenetics #Science
Feedback requested:
What would you improve?
#Structome #StructuralPhylogenetics #Science
#Structome began as an initiative to explore #evolutionary signals from #proteins sharing a structural neighborhood. It uses Q-score to rapidly gather datasets & build NJ trees. To highlight usage of Q-score, the tool is now called Structome-Q. App available here: biosig.lab.uq.edu.au/structome_q/
Structome-Q
Structome-Q: A next-generation platform for structural phylogenetics, enabling protein structure comparison, phylogenetic tree construction, and insights into deep evolutionary relationships.
biosig.lab.uq.edu.au
January 22, 2025 at 8:33 AM
#Structome began as an initiative to explore #evolutionary signals from #proteins sharing a structural neighborhood. It uses Q-score to rapidly gather datasets & build NJ trees. To highlight usage of Q-score, the tool is now called Structome-Q. App available here: biosig.lab.uq.edu.au/structome_q/
🌐 Structome-TM is freely available at
Structome-TM
Structome-TM: This resource complements Structome-Q in gathering protein structures and distance-based phylogenetic tree reconstruction.
biosig.lab.uq.edu.au
March 2, 2026 at 11:02 AM
🌐 Structome-TM is freely available at
Structome-TM enables phylogeny-ready structural dataset assembly using TM-score to prioritise local similarity over size-penalized global metrics.
March 2, 2026 at 11:02 AM
Structome-TM enables phylogeny-ready structural dataset assembly using TM-score to prioritise local similarity over size-penalized global metrics.
Structome-TM: complementing dataset assembly for structural phylogenetics by addressing size-based biases https://pubmed.ncbi.nlm.nih.gov/42261334/
June 10, 2026 at 7:16 AM
Structome-TM: complementing dataset assembly for structural phylogenetics by addressing size-based biases https://pubmed.ncbi.nlm.nih.gov/42261334/