title: Bioinformatics analysis of the epitope regions for norovirus capsid protein.
abstract: BACKGROUND
  Norovirus is the major cause of nonbacterial epidemic gastroenteritis, being highly prevalent in both developing and developed countries. Despite of the available monoclonal antibodies (MAbs) for different sub-genogroups, a comprehensive epitope analysis based on various bioinformatics technology is highly desired for future potential antibody development in clinical diagonosis and treatment.
  
  
  METHODS
  A total of 18 full-length human norovirus capsid protein sequences were downloaded from GenBank. Protein modeling was performed with program Modeller 9.9. The modeled 3D structures of capsid protein of norovirus were submitted to the protein antigen spatial epitope prediction webserver (SEPPA) for predicting the possible spatial epitopes with the default threshold. The results were processed using the Biosoftware.
  
  
  RESULTS
  Compared with GI, we found that the GII genogroup had four deletions and two special insertions in the VP1 region. The predicted conformational epitope regions mainly concentrated on N-terminal (1~96), Middle Part (298~305, 355~375) and C-terminal (560~570). We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup.
  
  
  CONCLUSIONS
  The predicted conformational epitope regions of norovirus VP1 mainly concentrated on N-terminal, Middle Part and C-terminal. We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup. The overlapping with experimental epitopes indicates the important role of latest computational technologies. With the fast development of computational immunology tools, the bioinformatics pipeline will be more and more critical to vaccine design.
authors.affiliation: Huzhou Center For Didsease Control and Preventron, Zhejiang 311000, China.
authors.forename: Liping
authors.initials: L
authors.lastname: Chen
authors.forename: Di
authors.initials: D
authors.lastname: Wu
authors.forename: Lei
authors.initials: L
authors.lastname: Ji
authors.forename: Xiaofang
authors.initials: X
authors.lastname: Wu
authors.forename: Deshun
authors.initials: D
authors.lastname: Xu
authors.forename: Zhiwei
authors.initials: Z
authors.lastname: Cao
authors.forename: Jiankang
authors.initials: J
authors.lastname: Han
mesh_terms: D000595:Amino Acid Sequence; D000914:Antibodies, Viral / Q000276:immunology; D017250:Caliciviridae Infections / Q000276:immunology / Q000821:virology; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics / Q000276:immunology*; D019295:Computational Biology; D000939:Epitopes / Q000737:chemistry / Q000235:genetics / Q000276:immunology*; D006801:Humans; D008969:Molecular Sequence Data; D029322:Norovirus / Q000235:genetics / Q000276:immunology*; D016415:Sequence Alignment
chemical_list: D000914:Antibodies, Viral; D036022:Capsid Proteins; D000939:Epitopes