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

  • Guy Grant
    ,
  • Birgit Albrecht
    ,
  • W. Graham Richards
  • University of Oxford
Research Output: Contribution to journal Article Peer-review

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 data sets 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.

Publication Information

Output type

Research Output: Contribution to journal Article Peer-review

Original language

English

Pages from-to (Number of pages)

Pages 425-432

Journal (Volume, Issue Number)

Protein Engineering, Design and Selection (Volume 17)

Publication milestones

  • Published - 01/01/2004

Publication status

Published - 01/01/2004

ISSN

1741-0126

External Publication IDs

  • handle.net: 10547/294865
  • Scopus: 4644334028

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