Identification of dna-binding and protein-binding proteins using enhanced graph wavelet features

Yuan Zhu, Weiqiang Zhou, Dao Qing Dai, Hong Yan

Research output: Contribution to journalArticlepeer-review


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).

Original languageEnglish (US)
Article number6606795
Pages (from-to)1017-1031
Number of pages15
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Issue number4
StatePublished - Jul 2013
Externally publishedYes


  • Protein-protein interaction
  • alpha shape model
  • graph wavelet
  • protein-DNA interaction

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Applied Mathematics


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