MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries

BMC Bioinformatics

Table 1 Test cases for validation and assessment of MimoPro

PDB_ID	antibody	antigen	Mimotopes^#	Ref
1JRH	A6, IgG1	IFNgammaR	59 × 5	[37]
1BJ1	rhuMAb	vascular endothelial growth factor	36 × 6, 3 × 5, 2 × 4	[38]
1G9M	17b	gp120	10 × 14, 1 × 12	[43]
1E6J	13B5	p24	14 × 14, 2 × 7	[43]
1N8Z	Herceptin	Her-2	5 × 12	[44]
1N8Z*	Herceptin	Her-2	8 × 12	[39]
1IQD	BO2C11	Coagulation factor VIII	27 × 12	[45]
1YY9	Cetuximab	Epidermal Growth Factor Receptor	3 × 10	[44]
2ADF	82D6A3, IgG	human von Willebrand factor (vWF)	2 × 15, 3 × 6	[46]
1ZTX	E16	West Nile Virus envelope glycoprotein(WNV E)	3 × 13, 19 × 14	[47]
3IU3	basiliximab	Interleukin-2 receptor subunit alpha	6 × 9	MS00013^$
2GHW	80R	Spike glycoprotein	9 × 16, 11 × 15, 17 × 14, 4 × 13	MS00059^$
2NY7	B12	Surface protein gp120	17 × 14, 1 × 10, 1 × 13	MS00056^$
Protein-protein interaction
1AVZ	Fyn	SH3 domain Nef Bovine	8 × 11, 10 × 12	[48]
1HX1	Hsc70	Bag chaperone regulator	8 × 15	[49]
1SQ0	Platelet glycoprotein Ib alpha chain	von Willebrand factor (vWF)	3 × 11	MS00465^$
1MQ8	ICAM-1	Integrin alpha-L beta-2	1 × 14	MS01004^$
1II4	FGFR-2	HBGF-2	30 × 7	MS01105/MS01110/MS01115^$

^# Number of peptides x peptide length
* 1N8Z* shares the same crystal complex with 1N8Z in PDB database.
^$ These cases are entries in a newly released database MimoDB [36] located at http://immunet.cn/mimodb/index.html.

ISSN: 1471-2105