ArticleMolecular biology and evolution2012
A stochastic evolutionary model for protein structure alignment and phylogeny.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Why structural divergence varies among residues in enzyme evolution: contributions of mutation, stability, and activity constraints.Molecular biology and evolution · 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
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Article
- A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins.Scientific reports · 2023Article
- Natural Selection on the Phase-Separation Properties of FUS during 160 My of Mammalian Evolution.Molecular biology and evolution · 2021Article
- Structural Phylogenetics with Confidence.Molecular biology and evolution · 2020Article
- Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States.Molecular biology and evolution · 2019Article
- Article
- The Enigmatic Origin of Papillomavirus Protein Domains.Viruses · 2017Article
- A Generative Angular Model of Protein Structure Evolution.Molecular biology and evolution · 2017Article
- Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions.Computational and structural biotechnology journal · 2017Article
- Phylogeny of Echinoderm Hemoglobins.PloS one · 2015Article
- Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure.Molecular biology and evolution · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein-Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution.
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