Geometry-based distance for clustering amino acids.

Clustering amino acids is one of the most challenging problems in functional and structural prediction of protein. Previous studies have proposed clusters based on measurements of physical and biochemical characteristics of the amino acids such as volume, area, hydrophilicity, polarity, hydrogen bonding, shape, and charge. These characteristics, although important, are less directly related to the protein structure compared to geometrical characteristics such as dihedral angles between amino acids.