Table 1
(continued)
Tool [reference]
URL (http or ftp)
Description
CLI
run
a
SSpro/ACCpro
[54]
http://scratch.proteomics.
ics.uci.edu
Surface accessibility prediction
Yes
3.4.1. Epitope prediction: MHC binding affinity
IEDB [55]
http://tools.iedb.org/main/
tcell/
Multiple methods for Epitope prediction
Yes
NetMHCpan [56] http://www.cbs.dtu.dk/
services/NetMHCpan/
Peptide-MHC Class I interaction predictions
integrating eluted ligand and peptide
binding affinity data
Yes
NetMHCIIpan
[57]
http://www.cbs.dtu.dk/
services/NetMHCIIpan/
Peptide-MHC class II binding prediction
Yes
NetMHCcons [58] http://www.cbs.dtu.dk/
services/NetMHCcons/
A consensus method for MHC class I
binding predictions
Yes
3.4.2. Epitope prediction: Structure-based antibody-binding regions
BEPPE [59]
http://bioinf.uab.es/
BEPPE/
Prediction of antigenic B- and T-cell epitopes
via Energy Decomposition Analysis
No
EDP [60]
Prediction of protein-protein interaction
sites using electrostatic desolvation profiles
No
3.5. Similarity with human proteins
NCBI
Blast vs. human
[11]
https://blast.ncbi.nlm.nih.
gov/
Sequence similarity search vs. human
genome
Yes
3.6. Antigen variability and epitope conservation among different genomes
Distmat
(EMBOSS) [61]
http://www.bioinformatics.
nl/cgi-bin/emboss/
distmat
Distance methods
Yes
MEGAX [62]
https://www.megasoftware.
net/
Distance methods
Yes
PVS (Protein
Variability
Server) [63]
http://imed.med.ucm.es/
PVS/
Site-by-site amino acid diversity
No
DnaSP [64]
http://www.ub.edu/dnasp/ Distance methods
No
PAML package
[65]
http://abacus.gene.ucl.ac.
uk/software/paml.html
Site-to-site variation in synonymous
substitution rate (Codeml)
Yes
HyPhy package
[66]
https://hyphy.org/
Site-to-site variation in synonymous
substitution rate (REL) and
recombination detection (GARD)
Yes
(continued)
Bacterial Pan-Proteome-Based Antigen Discovery
49