Predicting DNA binding protein-drug interactions based on network similarity

BMC Bioinformatics
Wei WangYuan Zhao

Abstract

The study of DNA binding protein (DBP)-drug interactions can open a breakthrough for the treatment of genetic diseases and cancers. Currently, network-based methods are widely used for protein-drug interaction prediction, and many hidden relationships can be found through network analysis. We proposed a DCA (drug-cluster association) model for predicting DBP-drug interactions. The clusters are some similarities in the drug-binding site trimmers with their physicochemical properties. First, DBPs-drug binding sites are extracted from scPDB database. Second, each binding site is represented as a trimer which is obtained by sliding the window in the binding sites. Third, the trimers are clustered based on the physicochemical properties. Fourth, we build the network by generating the interaction matrix for representing the DCA network. Fifth, three link prediction methods are detected in the network. Finally, the common neighbor (CN) method is selected to predict drug-cluster associations in the DBP-drug network model. This network shows that drugs tend to bind to positively charged sites and the binding process is more likely to occur inside the DBPs. The results of the link prediction indicate that the CN method has better predict...Continue Reading

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Methods Mentioned

BETA
X-ray
interaction prediction

Software Mentioned

Emig

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