Exploring the potential of 3D Zernike descriptors and SVM for protein–protein interface prediction

Daberdaku, Sebastian; Ferrari, Carlo

doi:10.1186/s12859-018-2043-3

BMC Bioinformatics

Table 5 The number of interface (positive samples) and non-interface (negative samples) local surface patches in the balanced and unbalanced versions of the training set and in the test set for each protein class

From: Exploring the potential of 3D Zernike descriptors and SVM for protein–protein interface prediction

Protein complex class	Receptor ligand	Bound unbound	Balanced training set			Unbalanced training set			Test set
			Interface patches	Non-interface patches	Total	Interface patches	Non-interface patches	Total	Interface patches	Non-interface patches	Total
A	r	b	4520	5859	10379	1162	31174	32336	629	22141	22770
		u	4545	5867	10412	1169	31070	32239	621	22315	22936
	l	b	4533	6164	10697	1155	32987	34142	674	20382	21056
		u	4809	5926	10735	1224	31529	32753	683	26222	26905
AB	r	b	2207	3806	6013	566	20284	20850	378	18852	19230
		u	2234	3805	6039	580	20181	20761	444	19265	19709
	l	b	2472	2315	4787	633	12329	12962	333	6175	6508
		u	2432	2319	4751	624	12316	12940	332	7877	8209
EI	r	b	8862	7350	16212	2254	39035	41289	1268	28696	29964
		u	7927	7350	15277	2026	38872	40898	1299	29502	30801
	l	b	11291	4172	15463	2890	22222	25112	1541	17243	18784
		u	13344	4170	17514	3397	22154	25551	1471	17085	18556
ER	r	b	5512	7404	12916	1392	39672	41064	1458	37028	38486
		u	5072	7418	12490	1295	39631	40926	1165	36294	37459
	l	b	7615	3779	11394	1953	20199	22152	973	13578	14551
		u	7218	3770	10988	1834	20293	22127	829	13053	13882
ES	r	b	2328	5429	7757	606	29129	29735	486	14498	14984
		u	1821	5361	7182	462	28721	29183	401	14013	14414
	l	b	3004	2231	5235	763	11934	12697	310	7704	8014
		u	2274	2227	4501	574	11866	12440	348	7658	8006
OG	r	b	3960	5557	9517	1008	29796	30804	873	18550	19423
		u	3469	5700	9169	882	30468	31350	764	19318	20082
	l	b	4501	2756	7257	1142	14773	15915	734	14996	15730
		u	3781	2803	6584	988	14887	15875	857	14844	15701
OR	r	b	5109	7344	12453	1298	39365	40663	696	19769	20465
		u	4218	7305	11523	1082	39031	40113	1079	19306	20385
	l	b	4691	3273	7964	1205	17471	18676	1012	14860	15872
		u	4163	3424	7587	1057	18219	19276	1635	14425	16060
OX	r	b	8894	10487	19381	2280	55923	58203	1831	62163	63994
		u	9096	10630	19726	2332	56765	59097	1591	62829	64420
	l	b	10146	8392	18538	2583	44821	47404	2035	32141	34176
		u	9560	9393	18953	2443	50234	52677	2119	33604	35723

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ISSN: 1471-2105

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