Novel drug-target interactions via link prediction and network embedding

BMC Bioinformatics

Table 1 Dataset details (a) Golden-standard dataset (b) ChEMBL-based dataset

(a) Golden_standarad_dataset	# Drug	# Target	# Negative/unknown DTI	# Positive interaction	Class ratio
Enzyme (E)	445	664	292,554	2926	0.01
Ion channel (IC)	210	204	41,364	1476	0.04
G-protein-coupled receptors (GPCR)	223	95	20,550	635	0.03
Nuclear receptor (NR)	54	26	1314	90	0.07
Total	791	989	777,172	5127	0.01

(b) ChEMBL_dataset	# Drug	# Target	# Real negative DTI^†	# Positive interaction*^{, †}	Class ratio
CheMBL	548	556	2057	1721	0.84
	# Weak DTI**	# Unknown DTI^‡
	532	300,378

^*pChEMBL value ≥ 5.5, **pChEMBL value > 0, ^†Development-dataset, ^‡Experimental-dataset

ISSN: 1471-2105