Geometrical comparison of two protein structures using Wigner-D functions

• Published in: Proteins, structure, function, and bioinformatics Vol. 82; no. 10; pp. 2756 - 2769
• Main Authors: Saberi Fathi, S. M., White, Diana T., Tuszynski, Jack A.
• Format: Journal Article
• Language: English
• Published: United States Blackwell Publishing Ltd 01.10.2014; Wiley Subscription Services, Inc
• Subjects: Algorithms; Animals; Computational Biology - methods; computational methods; correlation value; Crystallography, X-Ray; Databases, Protein; Fourier Analysis; Fourier transform; Humans; Models, Molecular; Molecular Weight; Poisson Distribution; protein classification; Protein Conformation; protein structure; Proteins - chemistry; Proteins - classification; reciprocal space; root-mean-square deviation; similarity value; Statistics as Topic; tubulin; Wigner-D functions; computational methods; protein structure; correlation value; similarity value; tubulin; Fourier transform; root-mean-square deviation; protein classification; reciprocal space; Wigner-D functions
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.24640

ABSTRACT 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.