Abstract
BackgroundProteins play a special role in bioinformatics. The surface shape of a protein, which is an important characteristic of the protein, defines a geometric and biochemical domain where the protein interacts with other proteins. The similarity analysis among protein models has become an important topic of protein analysis, by which it can reveal the structure and the function of proteins.ResultsIn this paper, a new protein similarity analysis method based on three-dimensional protein models is proposed. It constructs a feature matrix descriptor for each protein model combined by calculating the shape index (SI) and the related salient geometric feature (SGF), and then analyzes the protein model similarity by using this feature matrix and the extended grey relation analysis.ConclusionsWe compare our method to the Multi-resolution Reeb Graph (MRG) skeleton method, the L1-medial skeleton method and the local-diameter descriptor method. Experimental results show that our protein similarity analysis method is accurate and reliable while keeping the high computational efficiency.
Highlights
Proteins play a special role in bioinformatics
Motivated by the salient theory of a three-dimensional model proposed by Hoffman and Singh [16], and by the shape index (SI) concept by Bradford et al [17], we propose a new shape comparison method for three-dimensional protein models
We first estimate the curvature of each vertex on a protein model surface, and calculate the shape index (SI) and the salient geometric feature (SGF) based on the shape index of each vertex
Summary
The algorithm presented in this paper is implemented on a Intel(R) Core(TM) i3-3110 M CPU @2.5 Ghz desktop computer with 4GB RAM running MS Windows 7. The algorithm [13] based on the shape analysis by the local diameter construction resulted in a similarity of 0.9956, which is close to 1. It falsely reflects the similarity properties of the two proteins with different secondary structures. We conclude that our approach, in this specific case, improves the similarity analysis for non-homologous protein models with similar shapes
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