Measuring evolutionary rates of proteins in a structural context
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Updated: Feb 18, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Dariya K Sydykova1, Benjamin R Jack1, Stephanie J Spielman2
1Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA.
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.
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