Mature Epitope Density - A strategy for target selection based on immunoinformatics and exported prokaryotic proteins

Table 2 MED lowest-scored proteins.

Genome Locus	N	d	MED (nM/mer)	Local	Evidence	Unique publication identifier
Rv0532	59	555	3,19	SEC	contrary	10.1021/pr1005108
Rv0746	77	741	3,11	SEC	contrary	10.1186/1471-2148-6-95, 10.1016/j.micinf.2006.03.015
Rv1468c	37	328	3,03	SEC	contrary	10.1021/pr1005108
Rv3590c	48	542	2,96	SEC	favorable	10.1016/S1672-0229(08)60039-X
Rv3511	66	678	2,91	SEC	favorable	10.1186/1471-2148-6-95
Rv1100	20	160	2,88	PSE	contrary	10.1099/mic.0.27204-0
Rv3312A	4	64	2,69	SEC	contrary	10.1073/pnas.0602304104
Rv3595c	34	400	2,51	SEC	contrary	10.1186/1471-2148-6-95
Rv1091	60	814	2,40	SEC	contrary	10.1186/1471-2148-6-95
Rv3706c	4	50	2,32	PSE	contrary	10.3389/fmicb.2010.00121
Rv3345c	98	1498	2,05	SEC	favorable	10.1186/1471-2148-6-95, 10.1099/mic.0.26660-0
Rv0559c	4	78	2,05	SEC	contrary	10.1371/journal.pone.0007615
Rv3388	44	690	2,03	SEC	contrary	10.1016/j.tube.2003.12.014
Rv0833	52	689	1,75	PSE	favorable	10.1186/1471-2148-6-95
Rv2487c	28	655	1,15	SEC	contrary	Patent EP2207035
Rv3514	43	1448	0,93	SEC	contrary	10.1111/j.1365-2567.2010.03383.x
Rv3508	40	1860	0,71	SEC	contrary	10.1371/journal.pone.0002375, 10.1002/prot.10586
Rv3655c	0	0	0	PSE	contrary	10.1371/journal.pone.0010474

Table 2 lists 18 of the 30 MED lowest-scored proteins from the Mtb H37Rv exported proteins. Each protein is accompanied by at least a unique publication identifier, which can be doi, Pubmed id or a patent number. A protein can be cited twice or thrice by different publications; some publications cite several proteins. The first columns in Tables 1 and 2 show the protein locus tags, followed by the number of predicted epitopes (n) and epitope probability as a function of its proportion in the mature protein (d). The MED score is calculated as n divided by d. Evidence can be favorable or contrary based on publication results and the expectation indicated by the MED score.

ISSN: 1471-2164