title: NERVE: new enhanced reverse vaccinology environment.
abstract: BACKGROUND
  Since a milestone work on Neisseria meningitidis B, Reverse Vaccinology has strongly enhanced the identification of vaccine candidates by replacing several experimental tasks using in silico prediction steps. These steps have allowed scientists to face the selection of antigens from the predicted proteome of pathogens, for which cell culture is difficult or impossible, saving time and money. However, this good example of bioinformatics-driven immunology can be further developed by improving in silico steps and implementing biologist-friendly tools.
  
  
  RESULTS
  We introduce NERVE (New Enhanced Reverse Vaccinology Environment), an user-friendly software environment for the in silico identification of the best vaccine candidates from whole proteomes of bacterial pathogens. The software integrates multiple robust and well-known algorithms for protein analysis and comparison. Vaccine candidates are ranked and presented in a html table showing relevant information and links to corresponding primary data. Information concerning all proteins of the analyzed proteome is not deleted along selection steps but rather flows into an SQL database for further mining and analyses.
  
  
  CONCLUSIONS
  After learning from recent years' works in this field and analysing a large dataset, NERVE has been implemented and tuned as the first available tool able to rank a restricted pool (approximately 8-9% of the whole proteome) of vaccine candidates and to show high recall (approximately 75-80%) of known protective antigens. These vaccine candidates are required to be "safe" (taking into account autoimmunity risk) and "easy" for further experimental, high-throughput screening (avoiding possibly not soluble antigens). NERVE is expected to help save time and money in vaccine design and is available as an additional file with this manuscript; updated versions will be available at http://www.bio.unipd.it/molbinfo.
authors.affiliation: Molecular Biology and Bioinformatics (MOLBINFO), Department of Biology, University of Padua, viale G, Colombo 3, 35131 Padova, Italy. sandro@bio.unipd.it
authors.forename: Sandro
authors.initials: S
authors.lastname: Vivona
authors.forename: Filippo
authors.initials: F
authors.lastname: Bernante
authors.forename: Francesco
authors.initials: F
authors.lastname: Filippini
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000942:Antigens, Bacterial / Q000737:chemistry / Q000276:immunology; D001428:Bacterial Vaccines / Q000737:chemistry* / Q000276:immunology*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020407:Internet; D008969:Molecular Sequence Data; D020543:Proteome / Q000737:chemistry / Q000276:immunology; D012984:Software
chemical_list: D000942:Antigens, Bacterial; D001428:Bacterial Vaccines; D020543:Proteome