Identification of DNA-Binding and Protein-Binding Proteins Using Enhanced Graph Wavelet Features

Authors:
Yuan Zhu;Weiqiang Zhou;Dao-Qing Dai;Hong Yan
Affiliations:
Guangdong University of Finance and Economics, Guangzhou and Sun Yat-Sen University, Guangzhou;City University of Hong Kong, Hong Kong;Sun Yat-Sen University, Guangzhou;City University of Hong Kong, Hong Kong and University of Sydney, Sydney
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2013

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Abstract

Interactions between biomolecules play an essential role in various biological processes. For predicting DNA-binding or protein-binding proteins, many machine-learning-based techniques have used various types of features to represent the interface of the complexes, but they only deal with the properties of a single atom in the interface and do not take into account the information of neighborhood atoms directly. This paper proposes a new feature representation method for biomolecular interfaces based on the theory of graph wavelet. The enhanced graph wavelet features (EGWF) provides an effective way to characterize interface feature through adding physicochemical features and exploiting a graph wavelet formulation. Particularly, graph wavelet condenses the information around the center atom, and thus enhances the discrimination of features of biomolecule binding proteins in the feature space. Experiment results show that EGWF performs effectively for predicting DNA-binding and protein-binding proteins in terms of Matthew's correlation coefficient (MCC) score and the area value under the receiver operating characteristic curve (AUC).