{"id":"https://openalex.org/W4405544041","doi":"https://doi.org/10.1186/s12859-024-06004-0","title":"NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface","display_name":"NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface","publication_year":2024,"publication_date":"2024-12-18","ids":{"openalex":"https://openalex.org/W4405544041","doi":"https://doi.org/10.1186/s12859-024-06004-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/39695945"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-06004-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-06004-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-06004-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-06004-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Andrea Conte","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Andrea Conte","raw_affiliation_strings":["Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114710047","display_name":"Nicola Gulmini","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Nicola Gulmini","raw_affiliation_strings":["Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022531221","display_name":"Francesco Costa","orcid":"https://orcid.org/0000-0002-3719-6508"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["GB","IT"],"is_corresponding":false,"raw_author_name":"Francesco Costa","raw_affiliation_strings":["EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK","Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114710048","display_name":"Matteo Cartura","orcid":"https://orcid.org/0009-0005-2152-4406"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Matteo Cartura","raw_affiliation_strings":["Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026680264","display_name":"Felix Br\u00f6hl","orcid":"https://orcid.org/0000-0002-7343-3873"},"institutions":[{"id":"https://openalex.org/I4210087817","display_name":"Software (Germany)","ror":"https://ror.org/004g36n56","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210087817"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Felix Br\u00f6hl","raw_affiliation_strings":["Br\u00f6hl Software Development, Bonn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Br\u00f6hl Software Development, Bonn, Germany","institution_ids":["https://openalex.org/I4210087817"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021068227","display_name":"Francesco Patan\u00e8","orcid":"https://orcid.org/0009-0001-8619-447X"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesco Patan\u00e8","raw_affiliation_strings":["Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075029915","display_name":"Francesco Filippini","orcid":"https://orcid.org/0000-0001-5672-0726"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesco Filippini","raw_affiliation_strings":["Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy. francesco.filippini@unipd.it","Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy. francesco.filippini@unipd.it","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Padua, Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.2185,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.5913354,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"25","issue":"1","first_page":"378","last_page":"378"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.6202999949455261,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.6202999949455261,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10873","display_name":"Bacterial Infections and Vaccines","score":0.36059999465942383,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.005200000014156103,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6599977612495422},{"id":"https://openalex.org/keywords/reverse-vaccinology","display_name":"Reverse vaccinology","score":0.579425036907196},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.5435064435005188},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5286843180656433},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4652788043022156},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.45028218626976013},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.44327348470687866},{"id":"https://openalex.org/keywords/reverse-engineering","display_name":"Reverse engineering","score":0.43527457118034363},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.421170711517334},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3738126754760742},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.37292930483818054},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.3204660713672638},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2823055684566498},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.25480327010154724},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10633578896522522},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09666052460670471}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6599977612495422},{"id":"https://openalex.org/C2781152039","wikidata":"https://www.wikidata.org/wiki/Q7318278","display_name":"Reverse vaccinology","level":4,"score":0.579425036907196},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.5435064435005188},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5286843180656433},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4652788043022156},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.45028218626976013},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.44327348470687866},{"id":"https://openalex.org/C207850805","wikidata":"https://www.wikidata.org/wiki/Q269608","display_name":"Reverse engineering","level":2,"score":0.43527457118034363},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.421170711517334},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3738126754760742},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37292930483818054},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.3204660713672638},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2823055684566498},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.25480327010154724},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10633578896522522},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09666052460670471},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000078782","descriptor_name":"Vaccinology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000078782","descriptor_name":"Vaccinology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000078782","descriptor_name":"Vaccinology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000078782","descriptor_name":"Vaccinology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000078782","descriptor_name":"Vaccinology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000078782","descriptor_name":"Vaccinology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000078782","descriptor_name":"Vaccinology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-024-06004-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-06004-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-06004-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39695945","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39695945","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11654298","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11654298","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11654298/pdf/12859_2024_Article_6004.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.research.unipd.it:11577/3542425","is_oa":true,"landing_page_url":"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-06004-0","pdf_url":"https://www.research.unipd.it/bitstream/11577/3542425/2/s12859-024-06004-0.pdf","source":{"id":"https://openalex.org/S4377196283","display_name":"Research Padua  Archive (University of Padua)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:e0c205cc7c7c4903b27e1df7a00d77dc","is_oa":false,"landing_page_url":"https://doaj.org/article/e0c205cc7c7c4903b27e1df7a00d77dc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-20 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-06004-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-06004-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-06004-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321966","display_name":"Universit\u00e0 degli Studi di Padova","ror":"https://ror.org/00240q980"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405544041.pdf","grobid_xml":"https://content.openalex.org/works/W4405544041.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W216471693","https://openalex.org/W1972103487","https://openalex.org/W1996746577","https://openalex.org/W2049368529","https://openalex.org/W2067761505","https://openalex.org/W2090577544","https://openalex.org/W2097870001","https://openalex.org/W2102367710","https://openalex.org/W2124672930","https://openalex.org/W2134182833","https://openalex.org/W2138874847","https://openalex.org/W2152770371","https://openalex.org/W2156125289","https://openalex.org/W2157302781","https://openalex.org/W2158714788","https://openalex.org/W2161984798","https://openalex.org/W2162792752","https://openalex.org/W2171740232","https://openalex.org/W2585805431","https://openalex.org/W2588466226","https://openalex.org/W2755197481","https://openalex.org/W2793168264","https://openalex.org/W2793751297","https://openalex.org/W2898389621","https://openalex.org/W2900102202","https://openalex.org/W2914586483","https://openalex.org/W2917210380","https://openalex.org/W2918063357","https://openalex.org/W2945167000","https://openalex.org/W2950595506","https://openalex.org/W2984055282","https://openalex.org/W2996057451","https://openalex.org/W3006708056","https://openalex.org/W3128707844","https://openalex.org/W3131565611","https://openalex.org/W3162421907","https://openalex.org/W3164046276","https://openalex.org/W3184223611","https://openalex.org/W3186704098","https://openalex.org/W4235859326","https://openalex.org/W4309506674","https://openalex.org/W4378801524","https://openalex.org/W4387459704"],"related_works":["https://openalex.org/W1262800261","https://openalex.org/W2046452372","https://openalex.org/W3029677074","https://openalex.org/W2021824670","https://openalex.org/W2564391297","https://openalex.org/W2009867644","https://openalex.org/W2363997565","https://openalex.org/W1981120125","https://openalex.org/W3036615648","https://openalex.org/W4387276483"],"abstract_inverted_index":{"BACKGROUND:":[0],"Vaccines":[1],"development":[2,62,99],"in":[3,63],"this":[4],"millennium":[5],"started":[6],"by":[7,29,81,86],"the":[8,16,45,53,64,67,98,111,159,195],"milestone":[9],"work":[10],"on":[11,97],"Neisseria":[12],"meningitidis":[13],"B,":[14],"reporting":[15],"invention":[17],"of":[18,55,70,102,117,138,151,228],"Reverse":[19],"Vaccinology":[20],"(RV),":[21],"which":[22,109],"allows":[23,216],"to":[24,51,148,185,193,197,224],"identify":[25],"vaccine":[26,153,222],"candidates":[27,154],"(VCs)":[28],"screening":[30],"bacterial":[31,220],"pathogens":[32],"genome":[33],"or":[34,155],"proteome":[35],"through":[36],"computational":[37],"analyses.":[38],"When":[39],"NERVE":[40,103,182,214],"(New":[41],"Enhanced":[42],"RV":[43,47,75],"Environment),":[44],"first":[46],"software":[48],"integrating":[49],"tools":[50],"perform":[52],"selection":[54],"VCs,":[56],"was":[57,183],"released,":[58],"it":[59],"prompted":[60],"further":[61],"field.":[65],"However,":[66],"problem-solving":[68],"potential":[69],"most,":[71],"if":[72],"not":[73],"all,":[74],"programs":[76,131],"is":[77],"still":[78],"largely":[79],"unexploited":[80],"experimental":[82],"vaccinologists":[83],"that":[84],"impaired":[85],"somehow":[87],"difficult":[88],"interfaces,":[89],"requiring":[90],"bioinformatic":[91],"skills.":[92],"RESULTS:":[93],"We":[94,135],"report":[95],"here":[96],"and":[100,114,128,133,141,164,177,200,211,218],"release":[101],"2.0":[104,215],"(available":[105],"at:":[106],"https://nerve-bio.org":[107],")":[108],"keeps":[110],"original":[112],"integrative":[113],"modular":[115],"approach":[116],"NERVE,":[118],"while":[119],"showing":[120],"higher":[121],"predictive":[122],"performance":[123],"than":[124],"its":[125,139,209],"previous":[126],"version":[127],"other":[129],"web-RV":[130],"(Vaxign":[132],"Vaxijen).":[134],"renewed":[136],"some":[137],"modules":[140],"added":[142],"innovative":[143],"ones,":[144],"such":[145],"as":[146],"Loop-Razor,":[147],"recover":[149],"fragments":[150],"promising":[152],"Epitope":[156],"Prediction":[157],"for":[158],"epitope":[160],"prediction":[161],"binding":[162],"affinities":[163],"population":[165],"coverage.":[166],"Along":[167],"with":[168,190],"two":[169],"newly":[170],"built":[171],"AI":[172],"(Artificial":[173],"Intelligence)-based":[174],"models:":[175],"ESPAAN":[176],"Virulent.":[178],"To":[179],"improve":[180],"user-friendliness,":[181],"shifted":[184],"a":[186,191],"tutored,":[187],"web-based":[188],"interface,":[189],"noSQL-database":[192],"consent":[194],"user":[196],"submit,":[198],"obtain":[199],"retrieve":[201],"analysis":[202],"results":[203],"at":[204],"any":[205],"moment.":[206],"CONCLUSIONS:":[207],"With":[208],"redesigned":[210],"updated":[212],"environment,":[213],"customisable":[217],"refinable":[219],"protein":[221],"analyses":[223],"all":[225],"different":[226],"kinds":[227],"users.":[229]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
