A stochastic evolutionary model for protein structure alignment and phylogeny.

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Challis, CJ; Schmidler, SC

Published Date

  • November 2012

Published In

Volume / Issue

  • 29 / 11

Start / End Page

  • 3575 - 3587

PubMed ID

  • 22723302

Pubmed Central ID

  • PMC3697813

Electronic International Standard Serial Number (EISSN)

  • 1537-1719

International Standard Serial Number (ISSN)

  • 0737-4038

Digital Object Identifier (DOI)

  • 10.1093/molbev/mss167


  • eng