title: Geometrical comparison of two protein structures using Wigner-D functions.
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.
authors.affiliation: Department of Physics, Ferdowsi University of Mashhad, Mashhad, Iran.
authors.forename: S M
authors.initials: SM
authors.lastname: Saberi Fathi
authors.forename: Diana T
authors.initials: DT
authors.lastname: White
authors.forename: Jack A
authors.initials: JA
authors.lastname: Tuszynski
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D005583:Fourier Analysis; D006801:Humans; D008958:Models, Molecular; D008970:Molecular Weight; D016012:Poisson Distribution; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D013223:Statistics as Topic
chemical_list: D011506:Proteins
keywords: Fourier transform; Wigner-D functions; computational methods; correlation value; protein classification; protein structure; reciprocal space; root-mean-square deviation; similarity value; tubulin