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A stochastic evolutionary model for protein structure alignment and phylogeny

Publication ,  Journal Article
Challis, CJ; Schmidler, SC
Published in: Molecular Biology and Evolution
November 1, 2012

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. © 2012 The Author.

Duke Scholars

Published In

Molecular Biology and Evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

November 1, 2012

Volume

29

Issue

11

Start / End Page

3575 / 3587

Related Subject Headings

  • Stochastic Processes
  • Sequence Alignment
  • Rhodophyta
  • Proteins
  • Phylogeny
  • Phycocyanin
  • Models, Genetic
  • Humans
  • Hemoglobins
  • Genetic Variation
 

Citation

APA
Chicago
ICMJE
MLA
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Challis, C. J., & Schmidler, S. C. (2012). A stochastic evolutionary model for protein structure alignment and phylogeny. Molecular Biology and Evolution, 29(11), 3575–3587. https://doi.org/10.1093/molbev/mss167
Challis, C. J., and S. C. Schmidler. “A stochastic evolutionary model for protein structure alignment and phylogeny.” Molecular Biology and Evolution 29, no. 11 (November 1, 2012): 3575–87. https://doi.org/10.1093/molbev/mss167.
Challis CJ, Schmidler SC. A stochastic evolutionary model for protein structure alignment and phylogeny. Molecular Biology and Evolution. 2012 Nov 1;29(11):3575–87.
Challis, C. J., and S. C. Schmidler. “A stochastic evolutionary model for protein structure alignment and phylogeny.” Molecular Biology and Evolution, vol. 29, no. 11, Nov. 2012, pp. 3575–87. Scopus, doi:10.1093/molbev/mss167.
Challis CJ, Schmidler SC. A stochastic evolutionary model for protein structure alignment and phylogeny. Molecular Biology and Evolution. 2012 Nov 1;29(11):3575–3587.
Journal cover image

Published In

Molecular Biology and Evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

November 1, 2012

Volume

29

Issue

11

Start / End Page

3575 / 3587

Related Subject Headings

  • Stochastic Processes
  • Sequence Alignment
  • Rhodophyta
  • Proteins
  • Phylogeny
  • Phycocyanin
  • Models, Genetic
  • Humans
  • Hemoglobins
  • Genetic Variation