ImmunoNodes – graphical development of complex immunoinformatics workflows

BMC Bioinformatics

Table 1 Supported immunoinformatics methods sorted by field of application

Method	Version	Purpose	Reference
Epitope Prediction:
• BIMAS	1.0	MHC-I binding	[35]
• SVMHC	1.0	MHC-I binding	[36]
• ARB	1.0	MHC-I binding	[37]
• SMM	1.0	MHC-I binding	[38]
• SMMPMBEC	1.0	MHC-I binding	[39]
• Comblib 2008	1.0	MHC-I binding	[40]
• PickPocket	1.1	MHC-I binding	[34]
• NetMHC	4.0	MHC-I binding	[32]
• NetMHCpan	3.0	MHC-I binding	[41]
• HAMMER	1.0	MHC-II binding	[42]
• TEPITOPEpan	1.0	MHC-II binding	[43]
• NetMHCII	2.2	MHC-II binding	[44]
• NetMHCIIpan	3.1	MHC-II binding	[45]
• SYFPEITHI	1.0	T-cell epitope	[46]
• UniTope	1.0	T-cell epitope	[25]
• NetCTLpan	1.1	T-cell epitope	[47]
• Callis propensity	1.0	T-cell epitope/Immunogenicity	[48]
Cleavage Prediction:
• ProteaSMM (C/S20)	1.0	Cleavage site	[49]
• PCM	1.0	Cleavage site	[50]
• NetChop	3.1	Cleavage site	[51]
TAP Prediction:
• SVMTAP	1.0	TAP affinity	[50]
• SMMTAP	1.0	TAP affinity	[52]
• Additive matrix	1.0	TAP affinity	[53]
Epitope Selection:
• OptiTope	1.0	Epitope selection for vaccine design	[21]
Epitope Assembly:
• TSP approach	1.0	String-of-beads design	[22]
• Spacer design + TSP	1.0	Spacer design	[24]
HLA Typing:
• OptiType	1.0	MHC-I typing	[54]
• Seq2HLA	2.2	MHC-I/II typing	[55]

ISSN: 1471-2105