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.
Cite
@article{arxiv.1311.6771,
title = {Geometrical comparison of two protein structures using Wigner-D functions},
author = {Seyed Majid S. M. Saberi Fathi and Jack A Tuszynski},
journal= {arXiv preprint arXiv:1311.6771},
year = {2013}
}