Geometrical comparison of two protein structures using Wigner-D functions

Seyed Majid S. M. Saberi Fathi (1) , Jack A Tuszynski (2)

1 Department of Physics - Department of Physics
2 University of Alberta

In this paper, we develop a quantitative comparison method for two arbitrary protein structures. This method uses a root-mean-square deviation (RMSD) 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.

Mots clés: Protein structure; protein classification; computational methods; Wigner-D functions; root-mean-square deviation; tubulin; Fourier transform; reciprocal space; similarity value; correlation value

Domaines: Biophysique [physics.bio-ph]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Bio-informatique [q-bio.QM]

Seyed Majid S. M. Saberi Fathi, Jack A Tuszynski. Geometrical comparison of two protein structures using Wigner-D functions. 2013. ⟨hal-00909791v2⟩