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Journal of Molecular Evolution

, Volume 77, Issue 4, pp 159–169 | Cite as

Unearthing the Root of Amino Acid Similarity

  • James D. StephensonEmail author
  • Stephen J. Freeland
Original Article

Abstract

Similarities and differences between amino acids define the rates at which they substitute for one another within protein sequences and the patterns by which these sequences form protein structures. However, there exist many ways to measure similarity, whether one considers the molecular attributes of individual amino acids, the roles that they play within proteins, or some nuanced contribution of each. One popular approach to representing these relationships is to divide the 20 amino acids of the standard genetic code into groups, thereby forming a simplified amino acid alphabet. Here, we develop a method to compare or combine different simplified alphabets, and apply it to 34 simplified alphabets from the scientific literature. We use this method to show that while different suggestions vary and agree in non-intuitive ways, they combine to reveal a consensus view of amino acid similarity that is clearly rooted in physico-chemistry.

Keywords

Amino acids Simplified alphabets Similarity measures Chemical properties Protein structure 

Notes

Acknowledgments

This material is based upon work supported by the National Aeronautics and Space Administration through the NASA Astrobiology Institute under Cooperative Agreement No. NNA09DA77A issued through the Office of Space Science.

Supplementary material

239_2013_9565_MOESM1_ESM.pdf (235 kb)
Supplementary material 1 (PDF 236 kb)

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.NASA Astrobiology InstituteUniversity of HawaiiHonoluluUSA

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