Measuring evolutionary rates of proteins in a structural context

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 . In addition to describing the dN/dS specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses. Claus O. Wilke ( ) Corresponding author: [email protected] : Conceptualization, Methodology, Resources, Software, Validation, Visualization, Writing – Original Draft Author roles: Sydykova DK Preparation, Writing – Review & Editing; : Conceptualization, Methodology, Resources, Software, Validation, Visualization, Writing – Jack BR Original Draft Preparation, Writing – Review & Editing; : Conceptualization, Methodology, Resources, Software, Validation, Writing – Spielman SJ Original Draft Preparation, Writing – Review & Editing; : Conceptualization, Funding Acquisition, Methodology, Writing – Original Draft Wilke CO Preparation, Writing – Review & Editing No competing interests were disclosed. Competing interests: Sydykova DK, Jack BR, Spielman SJ and Wilke CO. How to cite this article: Measuring evolutionary rates of proteins in a structural 2017, :1845 (doi: ) context [version 1; referees: 1 approved] F1000Research 6 10.12688/f1000research.12874.1 © 2017 Sydykova DK . This is an open access article distributed under the terms of the , Copyright: et al Creative Commons Attribution Licence which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This work was supported by National Science Foundation Cooperative (agreement no. DBI-0939454; BEACON Center), Grant information: National Institutes of Health (grant R01 GM088344), and Army Research Office (grant W911NF-12-1-0390). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 16 Oct 2017, :1845 (doi: ) First published: 6 10.12688/f1000research.12874.1 1 1 2