An Empirical Study of Different Approaches for Protein Classification

Table 1

Summarized description of the datasets (if available, the number of training and independent samples is given in column “number of samples”). The column BKB reports whether it is possible from the dataset to obtain the PDB of the proteins for extracting the backbone structure.

Name	Short name	Number of samples	Number of classes	Protocol	BKB
Membrane subcellular	MEM	3249 + 4333	8	Independent training and testing sets	NO
Human pairs	HU	1882	2	10-fold cross validation	NO
Protein fold	PF	698	27	Independent training and testing sets	YES
GPCR	GP	730	2	10-fold cross validation	NO
GRAM	GR	452	5	10-fold cross validation	NO
Viral	VR	112	4	10-fold cross validation	NO
Cysteines	CY	957	3	10-fold cross validation	YES
SubCell	SC	121	3	10-fold cross validation	YES
DNA-binding proteins	DNA	349	2	10-fold cross validation	YES
Enzyme	ENZ	1094	6	10-fold cross validation	YES
GO dataset	GO	168	4	10-fold cross validation	YES
Human interaction	HI	8161	2	10-fold cross validation	NO
Submitochondria locations	SL	317	3	10-fold cross validation	NO
Virulent independent set 1	VI1	2055 + 83	2	Independent training and testing sets	NO
Virulent independent set 2	VI2	2055 + 284	2	Independent training and testing sets	NO
Adhesins	AD	2055 + 1172	2	Independent training and testing sets	NO