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Identification of DNA-Binding and Protein-Binding Proteins Using Enhanced Graph Wavelet Features
July-Aug. 2013 (vol. 10 no. 4)
pp. 1017-1031
Yuan Zhu, Dept. of Math., Guangdong Univ. of Finance & Econ., Guangzhou, China
Weiqiang Zhou, Dept. of Electron. Eng., City Univ. of Hong Kong, Kowloon, China
Dao-Qing Dai, Dept. of Math., Sun Yat-Sen Univ., Guangzhou, China
Hong Yan, Dept. of Electron. Eng., City Univ. of Hong Kong, Kowloon, China
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).
Index Terms:
proteins,biological techniques,biology computing,DNA,graph theory,molecular biophysics,receiver operating characteristic,DNA-binding proteins,protein-binding proteins,enhanced graph wavelet features,biomolecule interactions,machine learning based techniques,complex interface,feature representation method,biomolecular interfaces,graph wavelet theory,EGWF,interface feature,physicochemical features,graph wavelet formulation,protein feature discrimination,biomolecule binding proteins,area under ROC curve,Proteins,Educational institutions,Bioinformatics,Feature extraction,Computational biology,Correlation,Atomic measurements,alpha shape model,Protein-protein interaction,protein-DNA interaction,graph wavelet
Citation:
Yuan Zhu, Weiqiang Zhou, Dao-Qing Dai, Hong Yan, "Identification of DNA-Binding and Protein-Binding Proteins Using Enhanced Graph Wavelet Features," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 4, pp. 1017-1031, July-Aug. 2013, doi:10.1109/TCBB.2013.117
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