Visualization of Protein Fold Space via Nonmetric Multidimensional Scaling

Qiang      Xu

doi:10.2174/0929866054395257

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.

Keywords: protein fold, protein fold space, nonmetric multidimensional scaling, structure alignment

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Protein & Peptide Letters

Title: Visualization of Protein Fold Space via Nonmetric Multidimensional Scaling

Volume: 12 Issue: 5

Author(s): Qiang Xu

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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.

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Xu Qiang, Visualization of Protein Fold Space via Nonmetric Multidimensional Scaling, Protein & Peptide Letters 2005; 12 (5) . https://dx.doi.org/10.2174/0929866054395257