Measuring evolutionary rates of proteins in a structural context

Claus O. Wilke, Dariya K. Sydykova, Benjamin R. Jack, Stephanie J. Spielman

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations: One based on relative amino-acid rates, and the other based on site-specific codon rates measured as dN/ dS. We additionally provide a code repository containing scripts to facilitate the specific analysis protocols we recommend.

Original languageEnglish (US)
Article number1845
JournalF1000Research
Volume6
DOIs
StatePublished - 2018
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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