Inflammatory and Autoimmune Reactions in Atherosclerosis and Vaccine Design Informatics

Table 2

T-cell epitope prediction tools. This table, adapted from Table 1 [165], summarizes available websites for T-cell epitope prediction. The prediction mechanisms employed, URLs, or authors’ email addresses are included. Detailed descriptions and references are included in the paper.

Name	Description	URL
BIMAS	Half time dissociation to HLA class I molecules	http://thr.cit.nih.gov/molbio/hla_bind
EpiMatrix	Binding efficiency with MHC Class I and II	http://www.epivax.com/
FRAGPREDICT	Binding score of Proteasome Cleavage Sites	http://www.mpiib-berlin.mpg.de/MAPPP/cleavage.html
Immune Epitope Database and Analysis Resource (IEDB)	Analyze proteasomal processing, TAP transport, and MHC I&II binding to produce an overall score for a peptide’s potential for of being a T cell epitope	http://www.immuneepitope.org/
MHCPred	Based on MHC/peptide or TAP/peptide IC50 binding values	http://www.jenner.ac.uk/
MMBPred	Mutated high affinity MHC binding peptides	http://www.imtech.res.in/raghava/mmbpred/
NetChop	Proteasome or immunoproteasome cleavage sites	http://www.cbs.dtu.dk/services/NetChop/
NetCTL	Combined scores for MHC subtype binding, TAP transport and NetChop proteasome scores	http://www.cbs.dtu.dk/services/NetCTL/
NetMHC	MHC binding propensity of peptides	http:/www.cbs.dtu.dk/services/NetMHC
ProPred-1	Efficiency of MHC I peptide binding, optional proteasome/immunoproteasome cleavage filter	http://www.imtech.res.in/raghava/propred1
SYFPEITHI	Binding motifs to MHC Class I and II	http://syfpeithi.com
TAPPred	Binding affinity of TAP proteins	http://www.imtech.res.in/raghava/tappred/
TEPITOPE	Promiscuous MHC II epitopes	http://www.vaccinome.com/