QuaBingo: A Prediction System for Protein Quaternary Structure Attributes Using Block Composition

Table 2

Performance of using different features with SVM in 10-fold cross-validation for homo- and heterooligomer classification on the Oli8444 dataset.

	Homooligomer				Heterooligomer
	Sn (%)	Sp (%)	ACC (%)	MCC	Sn (%)	Sp (%)	ACC (%)	MCC
Block
Dimer	83.18	82.83	83.00	0.660	66.30	97.00	86.73	0.697
Trimer	89.25	99.76	95.48	0.909	83.65	97.50	91.93	0.835
Tetramer	75.32	97.53	90.12	0.776	85.03	98.03	92.82	0.853
Pentamer	100.00	96.67	98.57	0.973	83.33	95.00	89.17	0.813
Hexamer	89.03	98.52	94.27	0.887	82.50	97.00	90.42	0.812
Octamer	95.71	72.62	84.17	0.709	90.00	85.33	87.67	0.782
Decamer	91.67	100.00	95.83	0.928	100.00	100.00	100.00	1.000
Dodecamer	95.50	98.00	96.75	0.941	86.00	94.67	90.33	0.823
Overall			92.27	0.848			91.13	0.827
FunD
Dimer	52.49	90.26	71.37	0.462	74.74	90.16	85.01	0.659
Trimer	93.73	87.83	90.22	0.806	69.94	88.25	80.87	0.600
Tetramer	60.64	96.61	84.62	0.647	71.96	95.08	85.79	0.706
Pentamer	75.00	86.67	80.48	0.649	53.33	100.00	76.67	0.572
Hexamer	64.94	100.00	84.27	0.712	85.75	83.89	84.86	0.698
Octamer	48.81	100.00	74.40	0.566	44.67	100.00	72.33	0.517
Decamer	63.33	100.00	81.67	0.691	45.00	100.00	72.50	0.473
Dodecamer	63.00	100.00	81.50	0.680	69.00	100.00	84.50	0.733
Overall			81.07	0.652			80.32	0.620
PseASA
Dimer	66.95	46.74	56.85	0.140	12.62	93.07	66.18	0.094
Trimer	39.16	85.93	66.93	0.288	36.08	82.75	63.98	0.218
Tetramer	30.11	91.52	71.05	0.280	33.37	83.49	63.34	0.194
Pentamer	64.17	70.00	67.62	0.343	86.67	66.67	76.67	0.564
Hexamer	65.76	60.37	62.78	0.262	61.63	80.37	71.85	0.431
Octamer	66.90	60.48	63.69	0.285	86.00	71.50	78.75	0.604
Decamer	81.67	93.33	87.50	0.785	90.00	85.00	87.50	0.773
Dodecamer	73.50	68.00	70.75	0.429	66.83	85.50	76.17	0.556
Overall			68.40	0.352			73.05	0.429