Unearthing the Root of Amino Acid Similarity

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dc.contributor.authorStephenson, James D.
dc.contributor.authorFreeland, Stephen J.
dc.date.accessioned2022-03-28T14:48:48Z
dc.date.available2022-03-28T14:48:48Z
dc.date.issued2013-06-07
dc.description.abstractSimilarities 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.en_US
dc.description.sponsorshipThis 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.en_US
dc.description.urihttps://link.springer.com/article/10.1007/s00239-013-9565-0en_US
dc.format.extent11 pagesen_US
dc.genrejournal articlesen_US
dc.identifierdoi:10.13016/m2pq4q-eyle
dc.identifier.citationStephenson, J.D., Freeland, S.J. Unearthing the Root of Amino Acid Similarity. J Mol Evol 77, 159–169 (2013). https://doi.org/10.1007/s00239-013-9565-0en_US
dc.identifier.urihttps://doi.org/10.1007/s00239-013-9565-0
dc.identifier.urihttp://hdl.handle.net/11603/24443
dc.language.isoen_USen_US
dc.publisherSpringeren_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Individualized Study Program (INDS)
dc.rightsThis item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.en_US
dc.rightsAttribution 4.0 International (CC BY 4.0)*
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/*
dc.titleUnearthing the Root of Amino Acid Similarityen_US
dc.typeTexten_US

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