Ashar Malik
@proteinmechanic.bsky.social
Evolutionary Biologist | Protein Structure Enthusiast | Quantum Programmer | Wannabe Polymath | Science Comm | Life Sciences Programmer | Originally from 🇵🇰
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.
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.
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.
It’s like turning protein structures into a kind of “structural FASTA.” This lets us compare, align, and analyze proteins based on shape — not just sequence.
In the past www.biorxiv.org/content/10.1...
we used this method to character-based structural phylogenetic trees.
In the past www.biorxiv.org/content/10.1...
we used this method to character-based structural phylogenetic trees.
Tertiary-interaction characters enable fast, model-based structural phylogenetics beyond the twilight zone
Protein structure is more conserved than protein sequence, and therefore may be useful for phylogenetic inference beyond the “twilight zone” where sequence similarity is highly decayed. Until recently...
www.biorxiv.org
June 4, 2025 at 12:17 AM
It’s like turning protein structures into a kind of “structural FASTA.” This lets us compare, align, and analyze proteins based on shape — not just sequence.
In the past www.biorxiv.org/content/10.1...
we used this method to character-based structural phylogenetic trees.
In the past www.biorxiv.org/content/10.1...
we used this method to character-based structural phylogenetic trees.
What are structure-aware characters?
Structure-aware characters describe 3D conformation. Each residue gets a label (by Foldseek) based on its spatial context — enabling compact, alignment-ready strings from protein structures.
#Evolution #Phylogenetics #Science
Structure-aware characters describe 3D conformation. Each residue gets a label (by Foldseek) based on its spatial context — enabling compact, alignment-ready strings from protein structures.
#Evolution #Phylogenetics #Science
June 4, 2025 at 12:14 AM
What are structure-aware characters?
Structure-aware characters describe 3D conformation. Each residue gets a label (by Foldseek) based on its spatial context — enabling compact, alignment-ready strings from protein structures.
#Evolution #Phylogenetics #Science
Structure-aware characters describe 3D conformation. Each residue gets a label (by Foldseek) based on its spatial context — enabling compact, alignment-ready strings from protein structures.
#Evolution #Phylogenetics #Science
#DecodingEvolution The Molecular Story of Life’s Transformations
#Evolution is often seen in grand transformations dinosaurs into birds, fish onto land. Uncover how tiny changes drive life’s biggest adaptations, revealing evolution’s true blueprint.
pintofscience.com.au/event/from-m...
#Pint25
#Evolution is often seen in grand transformations dinosaurs into birds, fish onto land. Uncover how tiny changes drive life’s biggest adaptations, revealing evolution’s true blueprint.
pintofscience.com.au/event/from-m...
#Pint25
May 11, 2025 at 9:08 AM
#DecodingEvolution The Molecular Story of Life’s Transformations
#Evolution is often seen in grand transformations dinosaurs into birds, fish onto land. Uncover how tiny changes drive life’s biggest adaptations, revealing evolution’s true blueprint.
pintofscience.com.au/event/from-m...
#Pint25
#Evolution is often seen in grand transformations dinosaurs into birds, fish onto land. Uncover how tiny changes drive life’s biggest adaptations, revealing evolution’s true blueprint.
pintofscience.com.au/event/from-m...
#Pint25