ArticleMolecular biology and evolution2020
Structural Phylogenetics with Confidence.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Conserved protein folds underpin the diversification of secreted proteins in a fungal pathogen.BMC microbiology · 2026Article
- Protein Structure Characters in the Light of Phylogenetic Systematics.Genome biology and evolution · 2026Article
- Global approaches to infectious disease surveillance and modeling.Nature medicine · 2026Review
- The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.Archives of virology · 2026Article
- Evaluating the evolutionary relationship of TATA binding protein (TBP) with various folding patterns of protein domains using support vector machine (SVM).Scientific reports · 2026Article
- Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments.Genome biology and evolution · 2026Article
- Structome-TM: complementing dataset assembly for structural phylogenetics by addressing size-based biases.Bioinformatics advances · 2026Article
- MD-Phylogeny: Constructing Statistically Supported Phylogenetic Trees from Protein Structures Using Molecular Dynamics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Studying the Evolution of Protein Structure One Superfamily at a Time.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A Pipeline for Generating Datasets of Three-Dimensional Tertiary Interaction Characters for Model-Based Structural Phylogenetics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses.Nature structural & molecular biology · 2025Article
- Recent advances in the inference of deep viral evolutionary history.Journal of virology · 2025Review
- The Evolutionary History and Modern Diversity of Triterpenoid Cyclases.Molecular biology and evolution · 2025Article
- The evolutionary history and modern diversity of triterpenoid cyclases.bioRxiv : the preprint server for biology · 2025Article
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- A fast approach for structural and evolutionary analysis based on energetic profile protein comparison.Nature communications · 2025Article
- Faithful Interpretation of Protein Structures through Weighted Persistent Homology Improves Evolutionary Distance Estimation.Molecular biology and evolution · 2025Article
- Review
- multistrap: boosting phylogenetic analyses with structural information.Nature communications · 2025Article
- Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain.Journal of molecular evolution · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
For evaluating the deepest evolutionary relationships among proteins, sequence similarity is too low for application of sequence-based homology search or phylogenetic methods. In such cases, comparison of protein structures, which are often better conserved than sequences, may provide an alternative means of uncovering deep evolutionary signal. Although major protein structure databases such as SCOP and CATH hierarchically group protein structures, they do not describe the specific evolutionary relationships within a hierarchical level. Structural phylogenies have the potential to fill this gap. However, it is difficult to assess evolutionary relationships derived from structural phylogenies without some means of assessing confidence in such trees. We therefore address two shortcomings in the application of structural data to deep phylogeny. First, we examine whether phylogenies derived from pairwise structural comparisons are sensitive to differences in protein length and shape. We find that structural phylogenetics is best employed where structures have very similar lengths, and that shape fluctuations generated during molecular dynamics simulations impact pairwise comparisons, but not so drastically as to eliminate evolutionary signal. Second, we address the absence of statistical support for structural phylogeny. We present a method for assessing confidence in a structural phylogeny using shape fluctuations generated via molecular dynamics or Monte Carlo simulations of proteins. Our approach will aid the evolutionary reconstruction of relationships across structurally defined protein superfamilies. With the Protein Data Bank now containing in excess of 158,000 entries (December 2019), we predict that structural phylogenetics will become a useful tool for ordering the protein universe.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.