Junjie Xu
@for-surejjx.bsky.social
Reposted by Junjie Xu
Playing around with quantum-styled math on trivial biological problems before tackling the really hard questions. Initial signs are good, with the math behaving as expected. Next leg would be using a non-trivial dataset like missense variants.
On a quantum-inspired kernel for classifying protein torsion angles https://www.biorxiv.org/content/10.1101/2025.08.05.668681v1
August 7, 2025 at 1:11 PM
Playing around with quantum-styled math on trivial biological problems before tackling the really hard questions. Initial signs are good, with the math behaving as expected. Next leg would be using a non-trivial dataset like missense variants.
Reposted by Junjie Xu
Third Era of Phylogenetics!
1️⃣ Era 1: Morphology 🦴
2️⃣ Era 2: Sequences 🧬
3️⃣ Era 3: 3D Structures ⚛️
Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics
academic.oup.com/gbe/article/...
#structuralbiology #evolution #AlphaFold #SciSky
1️⃣ Era 1: Morphology 🦴
2️⃣ Era 2: Sequences 🧬
3️⃣ Era 3: 3D Structures ⚛️
Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics
academic.oup.com/gbe/article/...
#structuralbiology #evolution #AlphaFold #SciSky
Protein Structural Phylogenetics
Abstract. Protein structural phylogenetics is an interdisciplinary branch of molecular evolution that (i) uses 3D structural data to trace evolutionary his
academic.oup.com
August 22, 2025 at 12:40 AM
Third Era of Phylogenetics!
1️⃣ Era 1: Morphology 🦴
2️⃣ Era 2: Sequences 🧬
3️⃣ Era 3: 3D Structures ⚛️
Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics
academic.oup.com/gbe/article/...
#structuralbiology #evolution #AlphaFold #SciSky
1️⃣ Era 1: Morphology 🦴
2️⃣ Era 2: Sequences 🧬
3️⃣ Era 3: 3D Structures ⚛️
Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics
academic.oup.com/gbe/article/...
#structuralbiology #evolution #AlphaFold #SciSky
Reposted by Junjie Xu
Quantome: A Quantum Surrogate Model for Biophysical Landscapes https://www.biorxiv.org/content/10.1101/2025.08.06.668871v1
August 8, 2025 at 8:47 PM
Quantome: A Quantum Surrogate Model for Biophysical Landscapes https://www.biorxiv.org/content/10.1101/2025.08.06.668871v1
Reposted by Junjie Xu
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
Reposted by Junjie Xu
🧵: 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
Reposted by Junjie Xu
Using pairwise structure-aware character substitution scores across your proteins, the app computes per-column confidence, maps it to B-factors, and visualizes it in Mol*. You can spot conserved cores.
June 4, 2025 at 12:25 AM
Using pairwise structure-aware character substitution scores across your proteins, the app computes per-column confidence, maps it to B-factors, and visualizes it in Mol*. You can spot conserved cores.
Reposted by Junjie Xu
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.
Reposted by Junjie Xu
On interactive spatial visualisation of pathogenicity predictions https://www.biorxiv.org/content/10.1101/2025.03.19.644131v1
March 19, 2025 at 9:49 PM
On interactive spatial visualisation of pathogenicity predictions https://www.biorxiv.org/content/10.1101/2025.03.19.644131v1
Reposted by Junjie Xu
Missense mutations impact protein function, but no single predictor is perfect. MissenseViewer integrates AlphaMissense, ESM1b, and VESPA predictions, mapping them onto protein structures to provide a richer, more interpretable view of mutation effects.
#science #health #precisionmedicine #AI
#science #health #precisionmedicine #AI
On interactive spatial visualisation of pathogenicity predictions https://www.biorxiv.org/content/10.1101/2025.03.19.644131v1
March 19, 2025 at 10:59 PM
Missense mutations impact protein function, but no single predictor is perfect. MissenseViewer integrates AlphaMissense, ESM1b, and VESPA predictions, mapping them onto protein structures to provide a richer, more interpretable view of mutation effects.
#science #health #precisionmedicine #AI
#science #health #precisionmedicine #AI