Visualization of Protein Fold Space via Nonmetric Multidimensional Scaling

In this paper, a 3D map of protein fold space was produced using Dali structure alignment and nonmetric multidimensional scaling. The fold space comprises four radial clusters, which correspond to the four classes of SCOP. The overall structure of the protein fold space is largely determined by three factors: secondary structure composition, topology of β sheet, and domain size.