62. Kumar S, Stecher G, Li M, Knyaz C, Tamura
K (2018) MEGA X: molecular evolutionary
genetics analysis across computing platforms.
Mol Biol Evol 35:1547–1549
63. Garcia-Boronat M, Diez-Rivero CM, Reinherz EL, Reche PA (2008) PVS: a web server
for protein sequence variability analysis tuned
to facilitate conserved epitope discovery.
Nucleic Acids Res 36:W35–W41
64. Rozas J, Ferrer-Mata A, Sa ´nchez-DelBarrio
JC, Guirao-Rico S, Librado P, Ramos-Onsins
SE, Sa ´nchez-Gracia A (2017) DnaSP 6: DNA
sequence polymorphism analysis of large data
sets. Mol Biol Evol 34:3299–3302
65. Xu B, Yang Z (2013) PAMLX: a graphical
user interface for PAML. Mol Biol Evol
30:2723–2724
66. Pond SLK, Frost SDW, Muse SV (2005)
HyPhy: hypothesis testing using phylogenies.
Bioinformatics 21:676–679
67. Weaver S, Shank SD, Spielman SJ, Li M, Muse
SV, Kosakovsky Pond SL (2018) Datamonkey
2.0: a modern web application for characterizing selective and other evolutionary processes. Mol Biol Evol 35:773. https://doi.
org/10.1093/molbev/msx335
68. Baum BR (1989) PHYLIP: phylogeny inference package. Version 3.2. Joel Felsenstein. Q
Rev Biol 64:539–541
69. Guindon S, Dufayard J-F, Lefort V,
Anisimova M, Hordijk W, Gascuel O (2010)
New algorithms and methods to estimate
maximum-likelihood phylogenies: assessing
the performance of PhyML 3.0. Syst Biol
59:307–321
70. Kane TL, Carothers KE, Lee SW (2018) Virulence factor targeting of the bacterial pathogen Staphylococcus aureus for vaccine and
therapeutics. Curr Drug Targets 19:111–127
71. The Gene Ontology Consortium (2019) The
gene ontology resource: 20 years and still
GOing strong. Nucleic Acids Res 47:D330D338
72. El-Gebali S, Mistry J, Bateman A et al (2019)
The Pfam protein families database in 2019.
Nucleic Acids Res 47:D427–D432
73. Mitchell AL, Attwood TK, Babbitt PC et al
(2019) InterPro in 2019: improving coverage, classification and access to protein
sequence annotations. Nucleic Acids Res 47:
D351–D360
74. Carroll MC (2008) Complement and
Humoral Immunity. Vaccine 26:I28–I33
75. Backert L, Kohlbacher O (2015) Immunoinformatics and epitope prediction in the age of
genomic medicine. Genome Med 7:119
76. Gonzalez-Galarza FF, McCabe A, Melo Dos
Santos EJ, Takeshita L, Ghattaoraya G, Jones
AR, Middleton D (2018) Allele frequency net
database. Methods Mol Biol 1802:49–62
77. HLA allele frequencies and reference sets with
maximal population coverage. IEDB Solutions
us/articles/114094151851-HLA-allelefrequencies-and-reference-sets-with-maxi
mal-population-coverage. Accessed 26 Jun
2019
78. Greenbaum J, Sidney J, Chung J, Brander C,
Peters B, Sette A (2011) Functional classification of class II human leukocyte antigen
(HLA) molecules reveals seven different
supertypes and a surprising degree of repertoire sharing across supertypes. Immunogenetics 63:325–335
79. Weiskopf D, Angelo MA, de Azeredo EL et al
(2013) Comprehensive analysis of dengue
virus-specific
responses
supports
an
HLA-linked protective role for CD8+ T cells.
Proc Natl Acad Sci U S A 110:E2046–E2053
80. Lassaux P, Peri C, Ferrer-Navarro M et al
(2013) A structure-based strategy for epitope
discovery in Burkholderia pseudomallei OppA
antigen. Structure 21:167–175
81. Gourlay LJ, Peri C, Ferrer-Navarro M et al
(2013) Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for
structure-based epitope discovery/design in
structural
vaccinology.
Chem
Biol
20:1147–1156
82. Gourlay LJ, Thomas RJ, Peri C et al (2015)
From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK. FEBS J
282:1319–1333
83. Gaudesi D, Peri C, Quilici G et al (2015)
Structure-based design of a B cell antigen
from B. pseudomallei. ACS Chem Biol
10:803–812
84. van Gunsteren WF, Bakowies D, Baron R et al
(2006) Biomolecular modeling: goals, problems, perspectives. Angew Chem Int Ed
Eng 45:4064–4092
85. Telford JL (2008) Bacterial genome variability and its impact on vaccine design. Cell Host
Microbe 3:408–416
86. Khan AM, Hu Y, Miotto O, Thevasagayam
NM, Sukumaran R, Abd Raman HS, Brusic V,
Tan TW, Thomas August J (2017) Analysis of
viral diversity for vaccine target discovery.
BMC Med Genet 10:78
87. Graves CJ, Ros VID, Stevenson B, Sniegowski
PD, Brisson D (2013) Natural selection promotes antigenic evolvability. PLoS Pathog 9:
Bacterial Pan-Proteome-Based Antigen Discovery
61
K (2018) MEGA X: molecular evolutionary
genetics analysis across computing platforms.
Mol Biol Evol 35:1547–1549
63. Garcia-Boronat M, Diez-Rivero CM, Reinherz EL, Reche PA (2008) PVS: a web server
for protein sequence variability analysis tuned
to facilitate conserved epitope discovery.
Nucleic Acids Res 36:W35–W41
64. Rozas J, Ferrer-Mata A, Sa ´nchez-DelBarrio
JC, Guirao-Rico S, Librado P, Ramos-Onsins
SE, Sa ´nchez-Gracia A (2017) DnaSP 6: DNA
sequence polymorphism analysis of large data
sets. Mol Biol Evol 34:3299–3302
65. Xu B, Yang Z (2013) PAMLX: a graphical
user interface for PAML. Mol Biol Evol
30:2723–2724
66. Pond SLK, Frost SDW, Muse SV (2005)
HyPhy: hypothesis testing using phylogenies.
Bioinformatics 21:676–679
67. Weaver S, Shank SD, Spielman SJ, Li M, Muse
SV, Kosakovsky Pond SL (2018) Datamonkey
2.0: a modern web application for characterizing selective and other evolutionary processes. Mol Biol Evol 35:773. https://doi.
org/10.1093/molbev/msx335
68. Baum BR (1989) PHYLIP: phylogeny inference package. Version 3.2. Joel Felsenstein. Q
Rev Biol 64:539–541
69. Guindon S, Dufayard J-F, Lefort V,
Anisimova M, Hordijk W, Gascuel O (2010)
New algorithms and methods to estimate
maximum-likelihood phylogenies: assessing
the performance of PhyML 3.0. Syst Biol
59:307–321
70. Kane TL, Carothers KE, Lee SW (2018) Virulence factor targeting of the bacterial pathogen Staphylococcus aureus for vaccine and
therapeutics. Curr Drug Targets 19:111–127
71. The Gene Ontology Consortium (2019) The
gene ontology resource: 20 years and still
GOing strong. Nucleic Acids Res 47:D330D338
72. El-Gebali S, Mistry J, Bateman A et al (2019)
The Pfam protein families database in 2019.
Nucleic Acids Res 47:D427–D432
73. Mitchell AL, Attwood TK, Babbitt PC et al
(2019) InterPro in 2019: improving coverage, classification and access to protein
sequence annotations. Nucleic Acids Res 47:
D351–D360
74. Carroll MC (2008) Complement and
Humoral Immunity. Vaccine 26:I28–I33
75. Backert L, Kohlbacher O (2015) Immunoinformatics and epitope prediction in the age of
genomic medicine. Genome Med 7:119
76. Gonzalez-Galarza FF, McCabe A, Melo Dos
Santos EJ, Takeshita L, Ghattaoraya G, Jones
AR, Middleton D (2018) Allele frequency net
database. Methods Mol Biol 1802:49–62
77. HLA allele frequencies and reference sets with
maximal population coverage. IEDB Solutions
us/articles/114094151851-HLA-allelefrequencies-and-reference-sets-with-maxi
mal-population-coverage. Accessed 26 Jun
2019
78. Greenbaum J, Sidney J, Chung J, Brander C,
Peters B, Sette A (2011) Functional classification of class II human leukocyte antigen
(HLA) molecules reveals seven different
supertypes and a surprising degree of repertoire sharing across supertypes. Immunogenetics 63:325–335
79. Weiskopf D, Angelo MA, de Azeredo EL et al
(2013) Comprehensive analysis of dengue
virus-specific
responses
supports
an
HLA-linked protective role for CD8+ T cells.
Proc Natl Acad Sci U S A 110:E2046–E2053
80. Lassaux P, Peri C, Ferrer-Navarro M et al
(2013) A structure-based strategy for epitope
discovery in Burkholderia pseudomallei OppA
antigen. Structure 21:167–175
81. Gourlay LJ, Peri C, Ferrer-Navarro M et al
(2013) Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for
structure-based epitope discovery/design in
structural
vaccinology.
Chem
Biol
20:1147–1156
82. Gourlay LJ, Thomas RJ, Peri C et al (2015)
From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK. FEBS J
282:1319–1333
83. Gaudesi D, Peri C, Quilici G et al (2015)
Structure-based design of a B cell antigen
from B. pseudomallei. ACS Chem Biol
10:803–812
84. van Gunsteren WF, Bakowies D, Baron R et al
(2006) Biomolecular modeling: goals, problems, perspectives. Angew Chem Int Ed
Eng 45:4064–4092
85. Telford JL (2008) Bacterial genome variability and its impact on vaccine design. Cell Host
Microbe 3:408–416
86. Khan AM, Hu Y, Miotto O, Thevasagayam
NM, Sukumaran R, Abd Raman HS, Brusic V,
Tan TW, Thomas August J (2017) Analysis of
viral diversity for vaccine target discovery.
BMC Med Genet 10:78
87. Graves CJ, Ros VID, Stevenson B, Sniegowski
PD, Brisson D (2013) Natural selection promotes antigenic evolvability. PLoS Pathog 9:
Bacterial Pan-Proteome-Based Antigen Discovery
61