Prediction of B-cell Linear Epitopes with a Combination of Support Vector Machine Classification and Amino Acid Propensity Identification

Table 1

Epitopes predicted in the PC dataset after analysis with LEPS.

Antigen : length (UniProt ID^a)	LEPS-predicted Epitopes	Experimental epitopes	Ref.
PrP : 253; (P04156)	M1ANLGCWML9
		R37YPGQG42	[28]
		Q52GG54	[28]
		Q91GGGT95	[28]
		N100KPSKPKTNMKHMA113	[28]
		G123GLGGYMLG131	[28]
	S143DYEDRYYRENMHRYPN159	H140FGSDY 145	[28]
		Q160VYYRPMD167	[28]
		F198TETD202	[28]
	Y218ERESQAYYQRGS230
GAPDH : 338; (P20287)	A4KVGING10
	A21AFLKNTVDV30
	V31SVNDPFIDL40	V31SVNDPFIDLEYM43	[29]
	K48RDSTHGTFPGEVSTENGKLKVN	G58EVSTENGKLKVNGKLISVHCERDP82	[29]
	KL73
	C78ERDPANIPWDKDGA92
	A108QAHIKNNRAK118	G100VFTTIDKAQAHIKN114	[29]
	S123APSADAPM131
	V136NENSYEKS144
	V148SNASCTTN156
	K163VIHDKFEIV172	K163VIHDKFEIVE173	[29]
	V188VDGPSSKLWRDGRGAM204
	A210STGAAKAVG219
	L225NGKLT230
	R235VPTPDVSV243
	R249LGKGASYEE258
	F287VGSTSSS294	S268GPLKGILEYTEDEVVSSDFVG289	[29]
	I302SLNNNF308
	Y315DNEFGY321
	I329THMHKVDHA338
Ara h 1 : 626; (P43238)	K26SSPYQKKTENPC38	K26SSPYQKK33	[30]
	Q47QEPDDLK54	Q48EPDDLKQKA57	[30]
		E66YDPRCVY73	[30]
	P75RGHTGTTNQRSPPGERTRGRQPG	E90RTRGRQPGDYDDDRR105	[30]
	DYDDDRRQPRREEGGRWGPAGPRE	R108REEGGRW115	[30]
	REREEDWRQPREDWRRPSHQQPR	E124REEDWRQ131	[30]
	KIRPEGREGEQEWGTPGSHVREETSR	E134DWRRPSHQQPRKIRPEG151	[30]
	NN173
		P295GQFEDFF302	[30]
		Y312LQGFSRN319	[30]
		F325NAEFNEIRR334	[30]
		Q345EERGQRR352	[30]
	K381SVSKKGSEEEGDI394	D393ITNPINLRE402	[30]
		N409NFGKLFEVK418	[30]
		G463NLELV468	[30]
	K472EQQQRGRREEEEDEDEEEEGSN; EV497
		R498RYTARLKEG507	[30]
		E525LHLLGFGIN534	[30]
		H539RIFLAGDKD548	[30]
		I551DQIEKQAKDLAFPGSGE568	[30]
	P587QSQSQSPSSPEKESPEKEDQEEEN; QGGKGP617
SARS N : 422; (Q19QW0)		A36RPKQRRPQGLPNNTASWFT55	[31]
	H60GKEEL65
	T77NSGPDDQ84
	L140NTPKDHIGTRNPNNN155
		A156ATVLQLPQGTTLPKGFYAEGSRGG180	[31]
		T266KQYNVTQAFGRRGP280	[31]
		N286FGDQDLIRQGTDYK300	[31]
		K356HIDAYKTFPPTEPKKDKKK375	[31]
		R386QKKQPTVTLLPAADMDDFSRQLQN410	[31]
ZP3 : 399; (O77685, residue 24–422)	T31QSPAPGSSFSP42	T31QSPAPGSSFSPPPVVA47	[32]
		Q71AAELTLGPSACAPVPAEPLSK92	[32]
		H101ECGSELQMTPDSLIYSTVLHY122	[32]
	P124NLSQ128	L126SQSPLVLRSSP137	[32]
		G156IQPTWVPFHSTLSREQ172	[32]
		D251SSSIFISPRPG262	[32]
		V291TATDQAPSPLN302	[32]
		A311DEWLPVEGPRD322	[32]
		Q346EPGNPSEFEADLMLGPLVLSEAENGP372	[32]
AIV-H4 : 511; (A3KF09, residue17–527)	Q17NYTGNPVIC26	D107TCYPFDVPEYQSLR121	[33]
		F137QWNTVKQNGKSGACKRANVNDFFNRLNWLVK	[33]
	S169DGNAYP175	SDGNAYPLQNLTKINNGDYARLYIWGVHHPSTDT202
		N206LYKNNPGRVTVSTK220	[33]
		T224SVVPNIGSGPLVRGGQSGRVSXYWTIV250	[33]
		V257FNTIGNLIAPRGHYKLNNQKKSTILNTAIPIGSC; SKCHTDKGSLSTTKPFQNISRIAVGDCPRYV; QGSLKLATGMRNIPEKASRGLFGAI349	[33]
		D455SEMNKLFERVRRQL469	[33]
		A473EDKGNGCFEIFHKCDNN490	[33]
		N512RFQIQGVKLTQGYM526	[33]
AIV-H5 : 568; (A5HNY9)		A25NNSTEQVDTIMEKNVTVTHAQDILEKTHNGKL57	[33]
		E85FLNVPEWSYIVEKINPANDLCYP108	[33]
		C151PYQGRSSFFRNVVW165	[33]
		D199AAEQTRLYQNPTTY213	[33]
		R223SKVNGQSGRMEFFWTILKPNDAINFESNGNFIA	[33]
		ENAYKIV273
		L472RDNAKELGNGCFEFYHR489	[33]
	E284LEYGNCNTKC294
AIV-H12 : 527 (C7FPM3, residue 1–527)	T35LIEQNVPVT44	D31TVNTLIEQNVPVTQVEELVH51	[33]
		K127YERVKMFDFTKWNVTYTGTSKACNNTSNQGS	[33]
		YRSMRWLTLKSGQFPVQTDEY180
		F190TWAIHHPPTSDEQVKLYKNPNSLSSVTTDEINR	[33]
		FRPNIGPRPL234
		Q238QGRMDYYWAVLKPGQTV255	[33]
		T259NGNLIAPEYGHLITGKSHGRILKNDLPIGQCTTEC294	[33]
		T310SKHYIGKCPKYIPS324	[33]
		R334NVPQAQDRGLFGAIAGFIEG354	[33]
		I430TDIWAYNAELLVLLENQKTLDEHDANVRNLHD	[33]
		VR465
		G478CFEILHKCDDGCMDTIKNGT498	[33]
		Q502DYEEESKLERQRINGVKLEENSTYK527	[33]
DEN-3 E-glycoprotein : 493 (D2JWZ8, residue 281–773)		T331QLATLRKLCIEGKI345	[34]
		D351SRCPTQGEAVLPEEQDPNY370	[34]
		Q411YENLKYTVIITVHTGDQHQVGNETQGVT; AEITPQASTTE450	[34]
		L476LTMKNKAWMVHRQW490	[34]
	S533QEGA537	Q526EVVVLGSQEGAMHT540	[34]
	W669YKKGSSI676
	L707NSLG711
O. tsutsugamushi 47-kDa antigen : 466 (Q53246)		H21SKSLLNQKAVLPQQKSDMHIN42	[35]
		T65NIGISLNNKVSKYQQEV82	[35]
		V97TNENVIAGR106	[35]
		Y145ATFGDSNQS154	[35]
		V173TNGIISSKGRDMG186	[35]
		F193IQTNAAIHM202	[35]
		H201MGSFGGPMF210	[35]
		I233PSNTVLEAV242	[35]
	L245KKGEKIR252	L245KKGEKIRRG254	[35]
		L333LRNGKSMTLKCKIIANK350	[35]
		Q357SNDQSLVVN366	[35]
		L373TPDLVKKYNITSA386	[35]
HPV L1 protein : 510 (A8BQ01)		D41VYVTRTNVYYHGGSSRLLTVGHPYYSIKKSNN; VAVPKV80	[36]
	V122GRGQPL128	V90KLPDPNKFGLPDADLYDPDTQRLLWACVGVEVG; RGQPLGV130	[36]
		T205TIEDGDMVET215	[36]
		D219ICTNTCKYPDYLKMAAEPY238	[36]
		G235DSMFFSLRREQMFTRHFFNRGGKMGDTIPD285	[36]
	R326AQGHNNGMCW336
		S350TNVSLCATEA360	[36]
		F370KEYLRHMEEYDLQFIFQLCKITLTPEIMAY400	[36]
	V416PPPPSASL424
	K440PTPPKTPTDP450	P450YASLTFWDVDLSESFSMDLD470	[36]
	G497TPPPTSKRKRV508
Bacillus anthracis, PA domain III and IV : 248 (P13423, residue 488–735)	N538PSDPLETTKPDMT551	R532RIAAVNPSDPLETTKPDMT551	[37]
		A596ELNATNIYTVL607	[37]
		I620RDKRFHYDRNNIAVGADES639	[37]
		L692NISSLRQDGKT703	[37]
	N720PNYK724	L716YISNPNYKVNVYAVTKENT735	[37]

^aBecause some of the epitopes in the PC dataset were partial antigen fragments, the serial numbers for the residues in each epitope were assigned according to the sequence information retrieved from the UniProt database [38]. The overlapping amino acids between the experimentally verified and predicted epitopes are shown in bold.