In addition to the dataset used by Yamanishi et al. [14] , information about drug compounds and genes can be obtained from KEGG [46, 47] by the FTP operations: ftp://ftp.genome.jp/ pub/kegg/ligand/drug/drug for the drugs, and ftp://ftp.genome. jp/pub/kegg/genes/fasta/gene.pep for the genes. After excluding the drug-target pairs that lack experimental information, we finally obtained a total of 4,797 drug-target pairs, of which 2,719 for enzymes, 1,372 for ion channels, 630 for GPCRs, and 82 for nuclear receptors. All these datasets were used as the positive datasets in the current study.