Epipox is a resource customized for epitope vaccine design against pathogenic orthopoxviruses. The database is built upoen predicted T cell epitopes covering 124 proteins that are shared between the following orthopoxvirus:

Virus	STRAIN	ACC	Genes
Variola virus (VARV) major	Bangladesh-1975	L22579	189
VARV major	India-1967	NC_00161	197
VARV minor	Garcia-1966	Y16780	206
Monkeypox virus, MPXV	Zaire-96-I-16	NC_003310	191
Cowpox virus, CPXV	Brighton Red	AF482758	218
Vaccinia virus, VACV	Copenhagen	M35027	262
VACV	Tian Tan	AF095689	243
VACV	Ankara	U94848	157

The list of proteins that are equivalent between the selected orthopoxvirus can be obtained here

HLA

EPIPOX contains both CD4 and CD8 T cell epitopes that have been predicted using peptide-MHC I and II binding profiles, respectively . In particular, we used 32 HLA I and 33 HLA-II specific matrices. Users can select single of combination of HLA I molcules to retrieve the relevant T cell epitoptes. Here follow the list of HLA molecules in EPIPOX:

SUPERTYPES

A2: A*0201, A*0202, A*0203, A*0205, A*0206, A*0207, A6802
A3: A*0301, A*1101, A*3101, A*3301, A*6801, A*6601
A24: B*0702, B*3501, B*5101, B*5102, B*5301, B*5401

The alleles belogning to these supertypes are present in 88 % of the population regardless of their ething groups. Selecting promiscous peptides restricted by these 3 supertypes facilitate maximizaing the population coverage of vaccines with minimum number of peptides. For more details check Reche & Reche, NAR, 2005: W138-42

LIMITING SEARCH RESULTS

• LEADER: For selecting of proteins with leader peptide sequence
  • All: All proteins are selected
  • :T: Protein has a leader peptide sequence
  • :F: Protein does not have a leader peptide sequence
  
  
• TRANS: For selecting proteins with transmembrane regions
  • All: All proteins are selected
  • :T: Protein has predicted transmembrane region
  • :F: Protein does not have predicted transmembrane region
  
  
• ESPRESS: For selecting gene products according to temporal expression
  • All: All proteins are selected
  • E: Early expressed gene
  • I: Intermediate expressed gene
  • L: Intermediate expressed gene
  
  
• LOCATION: For selecting proteins located in virion (CORE) of membrane of infective forms.
  • All:All: All proteins are selected
  • CORE: Protein is part of the virion
  • IMV: Protein is located in the membrane of IMV form of the virus
  • EEV: Protein is located in the membrane of EEV form of the virus


• PCT OPT: For selecting epitopes with a given relative score. Each HLA-specific profile has a maximum a score and here users can select peptides with scores relative, expressed in percentange, to the maximum.


• CLEAVED:For HLA I-restricted epitopes is also selected those epitopes that are predicted to be generated by the proteasome:
  • All: All peptides are selected
  • T: Only peptides that predicted to be cleaved by the proteasome are selected