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Geometrical comparison of two protein structures using W igner‐D functions
Author(s) -
Saberi Fathi S. M.,
White Diana T.,
Tuszynski Jack A.
Publication year - 2014
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.24640
Subject(s) - series (stratigraphy) , root mean square , similarity (geometry) , square root , function (biology) , mathematics , wigner distribution function , protein structure , value (mathematics) , characterization (materials science) , square (algebra) , statistical physics , pure mathematics , mathematical analysis , computer science , physics , geometry , statistics , artificial intelligence , quantum , quantum mechanics , biology , nuclear magnetic resonance , evolutionary biology , optics , image (mathematics) , paleontology
In this article, we develop a quantitative comparison method for two arbitrary protein structures. This method uses a root‐mean‐square deviation characterization and employs a series expansion of the protein's shape function in terms of the Wigner‐D functions to define a new criterion, which is called a “similarity value.” We further demonstrate that the expansion coefficients for the shape function obtained with the help of the Wigner‐D functions correspond to structure factors. Our method addresses the common problem of comparing two proteins with different numbers of atoms. We illustrate it with a worked example. Proteins 2014; 82:2756–2769. © 2014 Wiley Periodicals, Inc.