Title: Visualization of Protein Fold Space via Nonmetric Multidimensional Scaling
VOLUME: 12 ISSUE: 5
Author(s):Qiang Xu
Affiliation:State Key Laboratory of Biomembrane and Membrane Biotechnology, Department of BiologicalSciences and Biotechnology, Tsinghua University, Beijing 100084, China.
Keywords:protein fold, protein fold space, nonmetric multidimensional scaling, structure alignment
Abstract: 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.
