Exploring the protein structure landscape for deep evolutionary signals. A suite of tools for structural phylogenetics, homology detection, and molecular evolution.
Interactive modules for building intuition about distance-based structural phylogenetics, including Module 4: The Resolution Limit (Duplicate Monophyly Criterion).
SMBE Australasian Protein Structural Phylogenetics Meeting. Thank you to all who attended.
Conference site →Quantifies conformational noise in 3Di and TEA structural alphabets using a new NNI metric and RF variance framework. bioRxiv, May 2026.
Read paper →Local similarity searches to identify homologs missed by global alignment. Accepts sequences with real-time structure prediction.
Rapid assembly of structural-neighbor datasets from a single query using global structural similarity.
Embedding-based pairwise distances for structural phylogenetics in high-dimensional space.
Protein language models and 3D structure to infer ancient protein evolutionary relationships.
Visualize and analyze structural alignments derived from character-based phylogenetic methods.
Quantifies conformational noise in structural alphabets (3Di, TEA) for phylogenetic inference using the NNI metric and RF variance framework.
Predicts SCOP, CATH, and ECOD structural classifications using structural profile HMMs.
Profile HMM-based structural homolog search using 3D coordinate information.
Structome-wide pairwise comparison database of 104 million protein chain pairs, classified by structural and sequence similarity across 61,631 representative PDB chains.
Exploring the protein structure landscape for deep evolutionary signals. A milestone timeline of tools, methods, and publications.
Interactive modules for building intuition about distance-based structural phylogenetics, including Module 4: The Resolution Limit (Duplicate Monophyly Criterion).
SMBE Australasian Protein Structural Phylogenetics Meeting. Thank you to all who attended.
Conference site →Quantifies conformational noise in 3Di and TEA structural alphabets using a new NNI metric and RF variance framework. bioRxiv, May 2026.
Read paper →Quantifies conformational noise in structural alphabets (3Di, TEA) for phylogenetic inference. Introduces the NNI metric and RF variance framework for principled alphabet comparison.
An empirical approach to bootstrapping distance-based structural phylogenies using synthetic taxon duplicates as internal calibration controls.
Local similarity-based homolog identification with real-time structure prediction from input sequences.
Visualization and analysis of structural alignments from character-based phylogenetic pipelines.
Structome-wide pairwise comparison database of 104 million protein chain pairs across 61,631 representative PDB chains, classified by structural and sequence similarity.
A comprehensive review on using protein structure for inferring deep evolutionary histories. Published in Genome Biology and Evolution.
Structural classification prediction (SCOP, CATH, ECOD) via profile HMMs derived from 3D structure.
Rapid structural-neighbor dataset assembly using global structural similarity from a single query protein.
Protein language models and 3D structure for inferring ancient protein evolutionary relationships.
Embedding-based pairwise distances for structural phylogenetics in high-dimensional latent space.
Profile HMM-based structural homolog search using information extracted from 3D coordinates.
Exploring the protein structure landscape for deep evolutionary signals — structural similarity, HMM profiling, and language model embeddings to resolve deep evolutionary histories.
Interactive modules for building intuition about distance-based structural phylogenetics, including Module 4: The Resolution Limit (Duplicate Monophyly Criterion).
SMBE Australasian Protein Structural Phylogenetics Meeting. Thank you to all who attended.
Conference site →Quantifies conformational noise in 3Di and TEA structural alphabets using a new NNI metric and RF variance framework. bioRxiv, May 2026.
Read paper →Local similarity searches to identify homologs often missed by global alignment. Expands Structome-Q by accepting protein sequences and predicting structures in real-time for immediate structural neighborhood analysis.
Global structural similarity for rapid structural-neighbor dataset assembly.
Embedding-based pairwise distances for structural phylogenetics.
Protein language models and 3D structure for inferring ancient protein evolutionary relationships.
Quantifies conformational noise in structural alphabets used for phylogenetic inference. Introduces the NNI metric and RF variance framework for principled comparison of coordinate-explicit alphabets (3Di) versus sequence-derived structure-aware alphabets (TEA). Companion to the Know Your Alphabet study.
Visualize and analyze structural alignments derived from character-based phylogenetic methods. Built to complement the character-based pipeline end-to-end.
SCOP, CATH, ECOD structural classification via structural profile HMMs.
Profile HMM-based structural homolog search using 3D coordinate information.
A pre-computed database of 104,528,817 unique pairwise comparisons across 61,631 UniProt-linked representative protein chains from the full experimental PDB. Each pair is classified on a two-axis landscape of structural similarity (Foldseek TM-score) and sequence similarity (BLASTP), with full feature vectors including rotation matrices for instantaneous structural superimposition.