A Novel Sequence-Based Feature for the Identification of DNA-Binding Sites in Proteins Using Jensen–Shannon Divergence
AbstractThe knowledge of protein-DNA interactions is essential to fully understand the molecular activities of life. Many research groups have developed various tools which are either structure- or sequence-based approaches to predict the DNA-binding residues in proteins. The structure-based methods usually achieve good results, but require the knowledge of the 3D structure of protein; while sequence-based methods can be applied to high-throughput of proteins, but require good features. In this study, we present a new information theoretic feature derived from Jensen–Shannon Divergence (JSD) between amino acid distribution of a site and the background distribution of non-binding sites. Our new feature indicates the difference of a certain site from a non-binding site, thus it is informative for detecting binding sites in proteins. We conduct the study with a five-fold cross validation of 263 proteins utilizing the Random Forest classifier. We evaluate the functionality of our new features by combining them with other popular existing features such as position-specific scoring matrix (PSSM), orthogonal binary vector (OBV), and secondary structure (SS). We notice that by adding our features, we can significantly boost the performance of Random Forest classifier, with a clear increment of sensitivity and Matthews correlation coefficient (MCC). View Full-Text
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Dang, T.K.L.; Meckbach, C.; Tacke, R.; Waack, S.; Gültas, M. A Novel Sequence-Based Feature for the Identification of DNA-Binding Sites in Proteins Using Jensen–Shannon Divergence. Entropy 2016, 18, 379.
Dang TKL, Meckbach C, Tacke R, Waack S, Gültas M. A Novel Sequence-Based Feature for the Identification of DNA-Binding Sites in Proteins Using Jensen–Shannon Divergence. Entropy. 2016; 18(10):379.Chicago/Turabian Style
Dang, Truong K.L.; Meckbach, Cornelia; Tacke, Rebecca; Waack, Stephan; Gültas, Mehmet. 2016. "A Novel Sequence-Based Feature for the Identification of DNA-Binding Sites in Proteins Using Jensen–Shannon Divergence." Entropy 18, no. 10: 379.
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