Measuring evolutionary rates of proteins in a structural context

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

doi:10.12688/f1000research.12874.1

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 journal › Article › peer-review

9 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. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses.

Original language	English (US)
Article number	1845
Journal	F1000Research
Volume	6
DOIs	https://doi.org/10.12688/f1000research.12874.1
State	Published - 2017
Externally published	Yes

All Science Journal Classification (ASJC) codes

General Biochemistry, Genetics and Molecular Biology
General Immunology and Microbiology
General Pharmacology, Toxicology and Pharmaceutics

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10.12688/f1000research.12874.1

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title = "Measuring evolutionary rates of proteins in a structural context",

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. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses.",

author = "Wilke, {Claus O.} and Sydykova, {Dariya K.} and Jack, {Benjamin R.} and Spielman, {Stephanie J.}",

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T1 - Measuring evolutionary rates of proteins in a structural context

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AU - Sydykova, Dariya K.

AU - Jack, Benjamin R.

AU - Spielman, Stephanie J.

PY - 2017

Y1 - 2017

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AB - 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. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses.

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JF - F1000Research

M1 - 1845

ER -

Measuring evolutionary rates of proteins in a structural context

Abstract

All Science Journal Classification (ASJC) codes

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