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PEDS Advance Access published online on June 8, 2004
Protein Engineering Design and Selection, doi:10.1093/protein/gzh049
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Received February 24, 2004
Revised May 17, 2004
Accepted May 21, 2004

Article

Evaluation of structural similarity based on reduced dimensionality representations of protein structure

Birgit Albrecht 1, Guy H. Grant 1, W. Graham Richards 1

1 Department of Chemistry, University of Oxford, Central Chemistry Laboratory, South Parks Road, Oxford, OX1 3QH, UK


  Abstract

Protein similarity estimations can be achieved using reduced dimensional representations and we describe a new application for the generation of two-dimensional maps from the three-dimensional structure. The code for the dimensionality reduction is based on the concept of pseudo-random generation of two-dimensional coordinates and Monte Carlo-like acceptance criteria for the generated coordinates.

A new method for calculating protein similarity is developed by introducing a distance dependent similarity field. Similarity of two proteins is derived from similarity field indices between amino acids based on various criteria such as hydrophobicity, residue replacement factors and conformational similarity, each showing a one factor Gaussian dependence.

Results on comparisons of misfolded protein models with datasets of correctly folded structures show that discrimination between correctly folded and misfolded structures is possible. Tests were carried out on five different proteins, comparing a misfolded protein structure with members of the same topology, architecture, family and domain according to the CATH classification.

Keywords: dimensionality reduction, molecular similarity, protein comparison, Sammon mapping


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