Volume 1 Supplement 1

BioSysBio 2007: Systems Biology, Bioinformatics, Synthetic Biology

Open Access

Discrimination of proteins using graph theoretic properties

BMC Systems Biology20071(Suppl 1):P49

DOI: 10.1186/1752-0509-1-S1-P49

Published: 8 May 2007

Background

Graph theoretic properties of proteins can be used to perceive the differences between correctly folded proteins and well designed decoy sets. Graphs are used to represent 3D protein structures. We used two different graph representations of protein structures which are Delaunay tessellations of proteins and contact map graphs. Graph theoretic properties for both graph types showed high classification accuracy to discrimination of proteins. Different type of linear classifiers and support vector classifier were used to classification of the protein structures. The best classifier accuracy was over 95% as shown in Table 1. The results showed that characteristic features of graph theoretic properties can be used many fields such as prediction of fold recognition, structure alignment and comparison, detection of similar domains and definition of structural motifs in high accuracy.
Table 1

:

 

Contact Map

Delaunay Tes.

 
 

After OA*

Before OA*

After OA*

Before OA*

Classifier Description

Svc

95,54%

94,12%

92,49%

90,67%

Support vector classifier

Klldc

95,22%

91,25%

82,97%

84,60%

Linear classifier by KL exp. of common cov matrix

Ldc

95,22%

91,25%

82,97%

84,60%

Normal densities based linear classifier

Pcldc

95,22%

91,25%

82,97%

84,60%

Linear classifier by PCA expansion on the joint data

Loglc

95,16%

93,68%

90,42%

87,07%

Logistic linear classifier

*OA: Outlier Analysis.

Conclusion

In this work we successfully showed that structural properties as well as potential scores can be used to discriminate native folds from the decoy sets. As far as graph types are concerned, the classification accuracy rates of the results obtained from contact map graphs are higher than the results obtained from Delaunay tessellated graphs for the same classification methods. Therefore contact map matrices are better representation method for protein structures. Support vector classifier and quadratic classifiers results are quite promising for the dataset which formed after outlier analysis. The accuracy rates are over 95%.

Authors’ Affiliations

(1)
Biological Sciences and Bioengineering, Sabanci University

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Copyright

© Küçükural and Sezerman; licensee BioMed Central Ltd. 2007

This article is published under license to BioMed Central Ltd.

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