Concerns that variola viruses might be used as bioweapons have renewed the interest in developing new and safer smallpox vaccines. Variola virus genomes are now widely available, allowing computational characterization of the entire T-cell epitome and the use of such information to develop safe and yet effective vaccines. To this end, we identified 124 proteins shared between various species of pathogenic orthopoxviruses including variola minor and major, monkeypox, cowpox, and vaccinia viruses, and we targeted them for T-cell epitope prediction. We recognized 8,106, and 8,483 unique class I and class II MHC-restricted T-cell epitopes that are shared by all mentioned orthopoxviruses. Subsequently, we developed an immunological resource, EPIPOX, upon the predicted T-cell epitome. EPIPOX is freely available online and it has been designed to facilitate reverse vaccinology. Thus, EPIPOX includes key epitope-focused protein annotations: time point expression, presence of leader and transmembrane signals, and known location on outer membrane structures of the infective viruses. These features can be used to select specific T-cell epitopes suitable for experimental validation restricted by single MHC alleles, as combinations thereof, or by MHC supertypes.
Smallpox was a devastating contagious disease that ravaged humankind for millennia, wiping out entire civilizations [
VARV belongs to the
As smallpox was eradicated and vaccination ceased, the global population has become increasingly susceptible to both smallpox and zoonosis by orthopoxviruses [
Immune protection against orthopoxviruses requires both B and T cells [
Advances in both immunology and genomic analysis offer new possibilities for eliciting immune protection without the requirement for live-virus vaccination and attendant complications. The identification of HLA class I and class II restricted T-cell epitopes (CD8 and CD4 T-cell epitopes, resp.) from poxviruses may allow us to develop safe and yet immunogenic peptide-based vaccines. Here, we describe the identification of protein antigens that are shared between several pathogenic orthopoxviruses, including VARV, MPXV, CPXV, and VACV, and T-cell epitopes that are identical in all selected proteins. This information was used to create a freely accessible web resource, EPIPOX: URL
In this study, we used the entire proteomes of 8 orthopoxviruses: VARV major, strain Bangladesh-1975, GenBank Accession: GB: L22579; VARV major, strain India-1967, GB: NC_00161; Variola major minor, strain Garcia-1966, GB: Y16780; Monkeypox virus, strain Zaire-96-I-16, GB: NC_003310; Cowpox virus strain, strain Brighton Red, GB: AF482758, Vaccinia virus, strain Copenhagen, GB: M35027; Vaccinia virus, strain Tian Tan, GB: AF095689; Vaccinia virus, strain Ankara, GB: U94848. The proteomes were obtained from the various translation features of the relevant GenBank genomic records using BIOPERL [
Orthopoxviruses used in this study.
Virus | Strain | ACC | Genes |
---|---|---|---|
VARV major | Bangladesh-1975 | L22579 | 189 |
VARV major | India-1967 | NC_00161 | 197 |
VARV minor | Garcia-1966 | Y16780 | 206 |
MPXV | Zaire-96-I-16 | NC_003310 | 191 |
CPXV | Brighton Red | AF482758 | 218 |
VACV | Copenhagen | M35027 | 262 |
VACV | Tian Tan | AF095689 | 243 |
VACV | Ankara |
U94848 | 157 |
We also used experimentally defined poxvirus-specific HLA I and HLA II-restricted T-cell epitopes that were retrieved from the IEDB [
We took VARV major, strain Bangladesh-1975, as the reference for subsequent sequence analyses. We identified proteins with leader signals using SIGNALP [
Information on the temporal expression of VACV genes was kindly provided by Dr. Lefkowitz from the Poxvirus Bioinformatics Resource Center [
We predicted MHC I and MHC II peptide binding to anticipate potential CD8 and CD4 T-cell epitopes, respectively. Specifically, we predicted peptide-MHC binding from VARV Bangladesh proteins that are shared between all selected orthopoxviruses using 32 HLA I- and 33 HLA II-allele specific position-specific scoring matrices (PSSMs) [
Predicted T-cell epitopes and obtained protein annotations were incorporated into a POSTGRES relational database. The database consists of 3 tables (
EPIPOX database structure. EPIPOX is a relational database consisting of three main tables:
T-cell adaptive immunity is required for clearance of poxviruses during infection and/or vaccination and can also contribute to protective immunity from subsequent exposures [
Nearly all orthopoxviruses can protect against challenge with another orthopoxvirus [
Orthopoxvirus proteins contributing to cross-protective immunity.
VACC: GI|ORF | VARV: GI|ORF | MPXV: GI|ORF | CPXV: GI|ORF | LOC1/EXP2/TM3/LD4 |
---|---|---|---|---|
335424|L1R | 438991|M1R | 17974993|M1R | 20153082|V099 | IMV/late/yes/no |
335455|D8L | 439016|F8L | 17975018|E8L | 20153106|V119 | IMV/late/yes/no |
335500|A27L | 439052|A31L | 17975052|A29L | 20153143|V156 | IMV/late/no/no |
335508|A33R | 439057|A36R | 17975058|A35R | 20153149|V162 | EEV/early/yes/no |
335549|B5R | 439084|B6R | 17975080|B6R | 20153177|V190 | EEV/#/yes/yes |
335438|H3L | 439004|I3L | 17975006|H3L | 20153094|V107 | IMV/late/yes/no |
335477|A10L | 439032|A11L | 17975034|A11L | 20153122|V135 | CORE/#/no/no |
335341|C7L | 438926|D11L | 17974926|D10L | 20153015|V028 | U/early/no/no |
Table shows GenBank identification numbers (GI) and open reading frame names (ORF) for VACC (strain Copenhagen), VARV (strain Bangladesh-1975), MPXV (strain Zaire-96-I-16), and CPXV (strain Brighton Red). 1LOC: location, 2EXP: temporal expression, 3TM: transmembrane, and 4LD: leader signal. NS: nonstructural gene. #: information not available. U: unknown. List of proteins was obtained from [
Shared orthopoxvirus proteins with transmembrane and/or leader sequences.
VARV GI|ORF | MPXV GI|ORF | CPXV GI|ORF | VACV GI|ORF | IDEN1 (%) | TM2 | LEAD3 | EXP4 | LOCATION5 |
---|---|---|---|---|---|---|---|---|
GI:439084|B6R | GI:17975080|B6R | GI:20153177|V190 | GI:335549|B5R | 93.1 | Yes | Yes | L | EEV membrane |
GI:439016|F8L | GI:17975018|E8L | GI:20153106|V119 | GI:335455|D8L | 94.7 | Yes | No | L | IMV membrane |
GI:438990|H9R | GI:17974992|G10R | GI:20153081|V094 | GI:335423|G9R | 98.1 | Yes | No | L | U |
GI:438919|D4R | GI:17974919|D3R | GI:20153007|V020 | GI:335333|C11R | 88.8 | Yes | Yes | U | U |
GI:439085|B7R | GI:17975081|B7R | GI:20153178|V191 | GI:335550|B6R | 93.1 | Yes | No | U | U |
GI:439035|A14L | GI:17975037|A14L | GI:20153125|V138 | GI:335483|A13L | 88.6 | Yes | No | L | IMV membrane |
GI:438946|C8L | GI:17974949|C10L | GI:20153036|V049 | GI:335366|F4L | 97.6 | Yes | No | E | U |
GI:438977|K5L | GI:17974979|I5L | GI:20153068|V081 | GI:335409|I5L | 94.9 | Yes | No | L | IMV membrane |
GI:438967|E8R | GI:17974969|F7R | GI:20153058|V071 | GI:335395|E8R | 97.4 | Yes | No | L | U |
GI:439004|I3L | GI:17975006|H3L | GI:20153094|V107 | GI:335438|H3L | 95.8 | Yes | No | L | IMV membrane |
GI:439014|F6R | GI:17975016|E6R | GI:20153104|V117 | GI:335453|D6R | 99.0 | Yes | No | L | U |
GI:439003|I2R | GI:17975005|H2R | GI:20153093|V106 | GI:335437|H2R | 99.2 | Yes | No | L | U |
GI:439056|A35L | GI:17975057|A34L | GI:20153148|V161 | GI:335506|A32L | 98.1 | Yes | No | L | U |
GI:439000|L5L | GI:17975002|L5L | GI:20153090|V103 | GI:335433|J5L | 98.1 | Yes | No | L | U |
GI:439058|A37R | GI:17975059|A36R | GI:20153150|V163 | GI:335509|A34R | 98.1 | Yes | No | L | EEV membrane |
GI:438991|M1R | GI:17974993|M1R | GI:20153082|V095 | GI:335424|L1R | 99.2 | Yes | No | L | IMV membrane |
GI:439057|A36R | GI:17975058|A35R | GI:20153149|V162 | GI:335508|A33R | 93.0 | Yes | No | E | EEV membrane |
GI:438951|C13L | GI:17974954|C15L | GI:20153041|V054 | GI:335373|F9L | 97.5 | Yes | No | L | U |
GI:439038|A17L | GI:17975040|A17L | GI:20153129|V142 | GI:335486|A16L | 97.0 | Yes | No | L | U |
GI:438974|K2L | GI:17974976|I2L | GI:20153065|V078 | GI:335405|I2L | 99.3 | Yes | No | L | U |
GI:439008|I7R | GI:17975010|H7R | GI:20153098|V111 | GI:335442|H7R | 95.2 | Yes | No | L | U |
GI:438982|H3L | GI:17974984|G2L | GI:20153073|V086 | GI:335414|G3L | 95.8 | Yes | No | L | U |
GI:439042|A22L | GI:17975044|A21L | GI:20153134|V147 | GI:335490|A21L | 96.9 | Yes | No | U | U |
GI:439059|A38R | GI:17975061|A38R | GI:20153152|V165 | GI:335512|A36R | 92.3 | Yes | No | E, L | EEV membrane |
GI:439031|A10L | GI:17975033|A10L | GI:20153121|V134 | GI:335476|A9L | 89.0 | Yes | Yes | E, L | U |
GI:439033|A12R | GI:17975035|A12R | GI:20153123|V136 | GI:335481|A11R | 98.5 | Yes | No | L | U |
GI:439036|A15L | GI:17975038|A15L | GI:20153126|V139 | GI:335484|A14L | 97.8 | Yes | No | L | IMV membrane |
GI:439067|A46R | GI:17975066|A43R | GI:20153159|V172 | GI:335522|A43R | 92.3 | Yes | Yes | U | U |
GI:439039|A18L | GI:17975041|A18L | GI:20153130|V143 | GI:335487|A17L | 98.0 | Yes | No | L | IMV membrane |
GI:439077|J7R | GI:17975076|B2R | GI:20153172|V185 | GI:335539|A56R | 82.1 | Yes | Yes | E, L | EEV membrane |
GI:439062|A41L | GI:17975063|A40L | GI:20153155|V168 | GI:335516|A38L | 94.7 | Yes | Yes | U | U |
Table shows GenBank identification numbers (GI) and open reading frame names (ORF) for VARV: strain Bangladesh-1975, MPXV: strain Zaire-96-I-16, CPXV: strain Brighton Red, and VACV: strain Copenhagen. 1IDEN: average identity between the selected proteins. 2TM: transmembrane. 3LEAD: leader signal. 4EXP: temporal expression (E: early, I: intermediate, and L: late). 5LOCATION: location.
We targeted the shared orthopoxvirus proteins for T-cell epitopes prediction using 32 and 33 HLA I- and HLA II-specific profile matrices (details in Material and Methods). The alleles targeted for peptide binding prediction are shown in Additional File S4. We selected these alleles because there are experimental peptide-binding data for them, which is required to make accurate peptide-MHC binding predictors [
We predicted a total of 18726 HLA I-restricted and 32722 HLA II-restricted orthopoxvirus specific T-cell epitopes, all being identical between all orthopoxviruses considered in this study. In Additional File S4 we provide numbers of T-cell epitopes predicted by each HLA-specific profile used in this study. We predicted more CD4 than CD8 T-cell epitopes because we used a more permissive peptide-binding threshold for MHC II molecules (4% of top scoring peptides) than for MHC I molecules (2% of top scoring peptides) since peptide-binding prediction to MHC II molecules is considerably less accurate than to MHC I molecules [
We compared the predicted T-cell epitome with experimentally defined poxvirus-specific HLA-restricted T-cell epitopes deposited in the IEDB [
Experimentally identified T-cell epitopes within the shared T-cell epitome predicted from pathogenic orthopoxvirus proteins.
CD8 T-cell epitopes | VARV GI | VARV ORF | Experimental HLA I restriction | Predicted HLA I restriction | |||||
---|---|---|---|---|---|---|---|---|---|
|
439013 | F5R | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | HLA-A6802 |
|
439056 | A35L | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | HLA-A6802 |
|
438985 | H5R | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | HLA-A6802 |
|
438979 | K7L | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | HLA-Cw0702 |
|
439072 | J2R | HLA-A0201 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | HLA-Cw0304 |
|
439004 | I3L | HLA-A0201 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | HLA-A0207 |
|
438965 | E6R | HLA-A0201 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | HLA-A0207 |
|
438988 | H7L | HLA-A0201 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | HLA-Cw0102 |
|
439072 | J2R | HLA-A2301 | HLA-A2301 | HLA-A2402 | HLA-A2403 | HLA-A2405 | HLA-A2407 | HLA-Cw0702 |
|
439046 | A25R | HLA-B7 | HLA-B0702 | HLA-B3501 | HLA-B5101 | HLA-B5301 | HLA-B5401 | HLA-Cw0102 |
|
439045 | A24R | HLA-A0201 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | HLA-A0207 |
|
438968 | E9L | HLA-B0702 | HLA-B0702 | HLA-B1502 | HLA-B3501 | HLA-B5101 | HLA-B5301 | HLA-B5401 |
|
438973 | K1L | HLA-A0201, HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | |
|
438985 | H5R | HLA-A0201, HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0205 | HLA-A0207 | HLA-Cw0702 | |
|
439009 | F1R | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | |
|
438960 | E1L | HLA-A2 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | HLA-Cw0304 | |
|
438994 | M4R | HLA-B07:02 | HLA-B0702 | HLA-B3501 | HLA-B4402 | HLA-B5301 | HLA-B5401 | |
|
438996 | L1R | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | |
|
439009 | F1R | HLA-A0201, HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | |
|
439025 | A4L | HLA-B07:02 | HLA-B0702 | HLA-B3501 | HLA-B5101 | HLA-B5301 | HLA-B5401 | |
|
439033 | A12R | HLA-B07:02 | HLA-B0702 | HLA-B3501 | HLA-B5101 | HLA-B5301 | HLA-B5401 | |
|
439007 | I6R | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | |
|
438998 | L3R | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0205 | HLA-A0206 | HLA-B1501 | |
|
438968 | E9L | HLA-B0702 | HLA-B0702 | HLA-B3501 | HLA-B5101 | HLA-B5301 | HLA-B5401 | |
|
439043 | A21R | HLA-A24, HLA-class I | HLA-A2301 | HLA-A2402 | HLA-A2403 | HLA-A2405 | HLA-A2407 | |
|
438980 | K8R | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | |
|
438981 | H1L | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0205 | HLA-A0206 | ||
|
439009 | F1R | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0205 | HLA-A0206 | ||
|
439029 | A8L | HLA-A0201 | HLA-A0201 | HLA-A0202 | HLA-A0205 | HLA-A0206 | ||
|
439043 | A21R | HLA-B3701 | HLA-B1501 | HLA-B1502 | HLA-B4402 | HLA-Cw0304 | ||
|
438934 | P1L | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0206 | ||
|
439036 | A15L | HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0205 | HLA-A0206 | ||
|
438981 | H1L | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0205 | HLA-A0207 | ||
|
438961 | E2L | HLA-B0702 | HLA-B0702 | HLA-B3501 | HLA-B5301 | HLA-B5401 | ||
|
438996 | L1R | HLA-A2 | HLA-A0201 | HLA-A0202 | HLA-A0206 | HLA-A6802 | ||
|
438979 | K7L | HLA-A0301, HLA-A1101 | HLA-A1101 | HLA-A3101 | HLA-A3301 | HLA-A6801 | ||
|
439029 | A8L | HLA-A0201 | HLA-A0201 | HLA-A0205 | HLA-A0207 | |||
|
439038 | A17L | HLA-A2 | HLA-A0201 | HLA-A0205 | HLA-A0206 | |||
|
438985 | H5R | HLA-A0301, HLA-A1101 | HLA-A3101 | HLA-A3301 | HLA-A6801 | |||
|
439066 | A45R | HLA-A2 | HLA-A0205 | HLA-A0207 | HLA-Cw0702 | |||
|
438955 | C17L | HLA-A2 | HLA-A0202 | HLA-A0203 | HLA-A0206 | |||
|
438952 | C14L | HLA-A2 | HLA-A0201 | HLA-A0205 | HLA-A6802 | |||
|
439045 | A24R | HLA-class I | HLA-A0201 | HLA-A0203 | HLA-A0206 | |||
|
439070 | A49R | HLA-A2, HLA-A0201 | HLA-A0202 | HLA-A0203 | HLA-A0206 | |||
|
439038 | A17L | HLA-A2 | HLA-A0202 | HLA-A0205 | HLA-A0206 | |||
|
438980 | K8R | HLA-A2 | HLA-A0202 | HLA-A0203 | HLA-A0205 | |||
|
439025 | A4L | HLA-B4403 | HLA-B4402 | HLA-B5801 | ||||
|
439029 | A8L | HLA-A2, HLA-A0201 | HLA-A0206 | HLA-Cw0304 | ||||
|
439040 | A19R | HLA-A1, HLA-class I | HLA-A0101 | HLA-B1501 | ||||
|
439019 | N1L | HLA-A2 | HLA-A0202 | HLA-A0205 | ||||
|
439014 | F6R | HLA-A0101, HLA-A3002 | HLA-A0101 | HLA-B1501 | ||||
|
439032 | A11L | HLA-A26, HLA-class I | HLA-A0101 | HLA-B5801 | ||||
|
439029 | A8L | HLA-A0201 | HLA-A0207 | HLA-A6802 | ||||
|
439030 | A9R | HLA-A2 | HLA-A0205 | HLA-A0206 | ||||
|
438973 | K1L | HLA-A0201 | HLA-A0203 | HLA-A0207 | ||||
|
439009 | F1R | HLA-A1, HLA-A2601, HLA-A2902 | HLA-A0101 | HLA-Cw0702 | ||||
|
439074 | J4R | HLA-B0801 | HLA-B0801 | |||||
|
473688 | L6R | HLA-A0201 | HLA-A0207 | |||||
|
439007 | I6R | HLA-A2 | HLA-A0202 | |||||
|
438942 | C4R | HLA-B1501 | HLA-A0203 | |||||
|
439009 | F1R | HLA-B4403 | HLA-B4402 | |||||
|
439028 | A7L | HLA-A2, HLA-A0201 | HLA-A0205 | |||||
|
439027 | A6R | HLA-A0101, HLA-A2902 | HLA-A0101 | |||||
|
438968 | E9L | HLA-A2, HLA-A02:01 | HLA-A0205 | |||||
|
439002 | I1L | HLA-B44 | HLA-B4402 | |||||
|
438980 | K8R | HLA-A2 | HLA-A0203 | |||||
|
438973 | K1L | HLA-A0201 | HLA-A0207 | |||||
|
439013 | F5R | HLA-A24, HLA-A2301, HLA-A2402 | HLA-Cw0702 | |||||
|
439014 | F6R | HLA-A0201 | HLA-Cw0102 | |||||
|
439043 | A21R | HLA-B3701 | HLA-B1501 | |||||
|
439022 | A1L | HLA-A0301, HLA-A1101 | HLA-B2705 | |||||
|
439045 | A24R | HLA-B4403 | HLA-B4402 |
CD4 T-cell epitope | VARV GI | VARV ORF | Experimental HLA II restriction | Predicted HLA II restriction | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
438960 | E1L | HLA-class II | DRB1 |
DRB1 |
DRB1 |
DRB1 |
DRB1 |
DRB1 |
DRB1 |
DRB1 |
DRB3 |
DRB5 |
|
439072 | J2R | DRB1 |
DRB1 |
DRB1 |
DRB1 |
DRB1 |
DRB3 |
|||||
|
439021 | N3L | DRB1 |
DRB1 |
DRB1 |
DRB3 |
|||||||
|
439066 | A45R | HLA-class II | DRB1 |
|||||||||
|
439021 | N3L | DRB1 |
DRB1 |
|||||||||
|
438934 | P1L | HLA-class II | DRB1 |
T-cell epitopes in this table are a subset of those provided in Additional File S1.
We developed a relational database based upon the predicted T-cell epitome and a web-based resource to facilitate online access and to query the database. We named this resource EPIPOX and made it available for free public use (URL:
The EPIPOX web interface (Figure
EPIPOX input page. The input page of EPIPOX is divided in two main sections for intuitive use. In the first part (SEARCH), users select HLA molecules and proteins to retrieve T-cell epitopes (multiple selection is allowed) while in the second part the user can limit the search output according to various criteria. These criteria include temporal expression of gene products (E: early; I: intermediate; L: late), location of proteins in relevant structures of the virus (CORE, IMV, and EEV), and the presence of leader and transmembrane regions. In addition, users can select only those peptides with a relative score above some selectable value. HLA-specific profiles used to score T-cell epitopes can reach a maximum score, which is used to set the relative score in percentage of each peptide. For HLA I-restricted epitopes, users can also restrict the search to those epitopes potentially generated by the proteasome.
EPIPOX result page. The figure shows a slice of the output resulting from promiscuous CORE protein peptides binding to the A2 supertype. The output consists of a tabulated list, with information on each of the fields of the search query (columns). From field
EPIPOX is related somewhat to certain existing databases. On the one hand, it shares features with generic epitope databases such as EPIMHC [
The availability of the VARV genomes enables the use of predictive tools that reveal entire T-cell epitomes and facilitate the development of epitope-based vaccines. However, in large and complex viruses, such as VARV, the potential T-cell epitome can be so sizeable that it will challenge experimental validation. Therefore, in this work we applied a rational strategy to limit the list of potential T-cell epitopes. First, we reduced the number of antigens by half by simply selecting those that are conserved among pathogenic orthopoxviruses related to VARV. Second, we enriched the antigens with annotations such as temporal expression and location. Lastly, we created a resource and
We expect that this work and EPIPOX will be instrumental in developing safer smallpox vaccines and thereby in preventing zoonosis caused by other orthopoxviruses, including MPXV, which is also a potential terrorist bioweapon. In the future, we plan to enhance EPIPOX with validated and/or experimentally determined epitopes, upgrade protein annotations with functional information, and include additional features such as TAP transport [
The authors declare that they have no conflict of interests.
The authors want to specially thank Dr. Ellis L Reinherz for his continuous support, inspiration, and future collaborative work. The authors also wish to thank