Algorithmic approaches to protein-protein interaction site prediction

Aumentado-Armstrong, Tristan T; Istrate, Bogdan; Murgita, Robert A

doi:10.1186/s13015-015-0033-9

Algorithms for Molecular Biology

Table 4 Comparative evaluation of recent predictors

From: Algorithmic approaches to protein-protein interaction site prediction

PredName	Year	Label	Dataset	Precision	Recall	Accuracy	AUC	MCC	F1	Source
ProMate	2004	A	DB3-188 ^†	36.5	30.3	77.1	67.7	19.5	33.1	[34]
		B	DS56B	31.9	27.3	76.7	63.3	15.6	29.4
		C	DS56U	28.7	27.3	76.6	62.7	14.0	28.0
		E	NI2	40.0	93.9	∗	∗	13.6	56.1	[37]
		F	PlaneDimers	∗	∗	∗	68.0	18.0	∗	[33]
		G	TransComp_1	∗	∗	∗	70.0	20.0	∗
ConsPPISP	2005	A	DB3-188 ^†	46.5	30.6	80.4	73.2	26.7	36.9	[34]
		B	DS56B	39.8	36.1	78.9	72.6	25.2	37.9
		C	DS56U	37.4	34.5	79.5	71.2	23.8	35.9
		E	NI2	49.3	32.2	∗	∗	14.7	39.0	[37]
PINUP	2006	A	DB3-188 ^†	40.7	34.7	78.3	66.0	24.6	37.5	[34]
		B	DS56B	37.3	31.9	78.4	63.7	21.7	34.4
		C	DS56U	30.4	30.1	76.9	60.0	16.4	30.2
		E	NI2	52.9	28.5	∗	∗	15.1	37.0	[37]
WHISCY	2006	H	W025	39.0	27.0	∗	∗	27.0	∗	[40]
metaPPISP	2007	A	DB3-188 ^†	49.0	26.7	81.1	74.6	26.2	34.6	[34]
		B	DS56B	43.3	25.8	80.8	74.4	22.9	32.3
		C	DS56U	38.9	24.0	81.1	71.5	20.2	29.7
		E	NI2	54.7	25.5	∗	∗	16.6	34.8	[37]
		F	PlaneDimers	∗	∗	∗	54.0	4.0	∗	[33]
		G	TransComp_1	∗	∗	∗	78.0	31.0	∗
PIER	2007	E	NI2	44.1	83.6	∗	∗	23.0	57.7	[37]
SPPIDER	2007	J	S149	63.7	60.3	∗	76.0	42.0	∗	[40]
		F	PlaneDimers	∗	∗	∗	80.0	33.0	∗	[33]
		G	TransComp_1	∗	∗	∗	68.0	15.0	∗
Sikic	2009	L	3DS	63.4	78.3	65.3	∗	30.8	∗	[38]
PredUs	2010	A	DB3-188	43.6	45.7	∗	∗	∗	∗	[31]
		B	DS56B	41.5	42.2	∗	∗	∗	∗
		C	DS56U	39.8	44.6	∗	∗	∗	∗
	2011	A	DB3-188	50.3	57.5	72.6	73.9	34.5	53.0	[32]
		B	DS56B	43.0	53.0	72.1	71.3	29.0	47.4
		C	DS56U	43.3	53.6	73.2	72.9	30.4	47.9
		K	S58	45.5	57.6	78.5	∗	37.7	50.8	[7]
VORFFIP	2011	J	S149	63.4	74.7	∗	90.0	58.0	∗	[40]
		H	W025	42.0	47.0	∗	∗	38.0	∗
		M	B100	45.0	56.0	∗	∗	42.0	49.0
HomPPI	2011	N	BM180 ¹	∗	58.0	85.0	∗	44.0	∗	[20]
			BM180 ²	∗	48.0	84.0	∗	42.0	∗
			BM180 ³	∗	71.0	86.0	∗	60.0	∗
			BM180 ⁴	∗	73.0	91.0	∗	65.0	∗
PrISE	2012	A	DB3-188 ^†	48.0	43.2	80.6	77.2	33.8	45.5	[34]
		B	DS56B	46.1	45.4	80.9	77.6	34.1	45.7
		C	DS56U	43.7	44.0	81.2	75.5	32.6	43.8
Li mRMR-IFS	2012	L	3DS	65.3	79.0	67.3	∗	34.8	∗	[38]
Chen PDM-ML	2012	I	S435 ^‡	51.2	66.2	75.9	∗	42.0	57.8	[7]
		J	S149 ^§	51.9	67.7	75.3	∗	42.3	58.8
		K	S58	44.6	65.4	77.7	∗	40.3	53.0
PresCont	2012	F	PlaneDimers	∗	∗	∗	80.0	33.0	∗	[33]
		G	TransComp_1	∗	∗	∗	69.0	17.0	∗
RAD-T	2014	A	DB3-188	28.5	64.7	65.2	∗	22.2	35.5	[37]
		D	NI1	33.8	80.5	51.8	∗	20.1	46.4
		E	NI2	44.7	80.9	59.1	∗	26.4	57.6

^†refers to the DB3-188 set excluding 2VIS; ^‡refers to the S435 set excluding 3 proteins due to obsolescence or absence; ^§refers to the S149 set excluding 7 proteins due to existence in training set. BM180 ¹ are transient enzyme-inhibitor complexes, BM180 ² are transient non-enzyme- inhibitor complexes, BM180 ³ are obligate hetero-dimers and BM180 ¹ are obligate homo-dimers.

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