{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T20:07:49Z","timestamp":1787170069056,"version":"build-2736575974"},"reference-count":48,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Microbiological Methods"],"published-print":{"date-parts":[[2025,11]]},"DOI":"10.1016\/j.mimet.2025.107268","type":"journal-article","created":{"date-parts":[[2025,9,22]],"date-time":"2025-09-22T21:08:11Z","timestamp":1758575291000},"page":"107268","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"special_numbering":"C","title":["Design and in silico evaluation of a novel chimeric protein vaccine candidate against Salmonella Typhi"],"prefix":"10.1016","volume":"238","author":[{"given":"Mohsen Bidar","family":"Ajerloo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abbas","family":"Hajizade","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shahram","family":"Nazarian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kavyan","family":"Khalili","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"1","key":"10.1016\/j.mimet.2025.107268_bb0005","doi-asserted-by":"crossref","first-page":"6432580","DOI":"10.1155\/2020\/6432580","article-title":"Extensively drug-resistant (XDR) typhoid: evolution, prevention, and its management","volume":"2020","author":"Akram","year":"2020","journal-title":"Biomed. Res. Int."},{"issue":"1","key":"10.1016\/j.mimet.2025.107268_bb0010","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1745-7580-6-6","article-title":"Identification of conformational B-cell epitopes in an antigen from its primary sequence","volume":"6","author":"Ansari","year":"2010","journal-title":"Immunome Res."},{"key":"10.1016\/j.mimet.2025.107268_bb0015","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/bs.mie.2020.10.003","article-title":"Design of helical linkers for fusion proteins and protein-based nanostructures","volume":"647","author":"Arai","year":"2021","journal-title":"Methods Enzymol."},{"issue":"4","key":"10.1016\/j.mimet.2025.107268_bb0020","doi-asserted-by":"crossref","first-page":"396","DOI":"10.3390\/vaccines12040396","article-title":"Vaccines induce homeostatic immunity, generating several secondary benefits","volume":"12","author":"Arunachalam","year":"2024","journal-title":"Vaccines"},{"issue":"5","key":"10.1016\/j.mimet.2025.107268_bb0025","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1016\/j.chom.2016.10.007","article-title":"The Salmonella effector SteD mediates MARCH8-dependent ubiquitination of MHC II molecules and inhibits T cell activation","volume":"20","author":"Bayer-Santos","year":"2016","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.mimet.2025.107268_bb0030","doi-asserted-by":"crossref","unstructured":"Bell ME, Haag M, Clasen SJ, B\u00f6cker M, Maksymenko K, Koch I, et al. Kinetic and structure-based comparisons of silent and stimulatory flagellin interactions with TLR5. bioRxiv 2024:2024.12. 09.627598.","DOI":"10.1101\/2024.12.09.627598"},{"issue":"7\u20138","key":"10.1016\/j.mimet.2025.107268_bb0040","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1080\/20477724.2024.2416864","article-title":"Combatting extensively drug-resistant Salmonella: a global perspective on outbreaks, impacts, and control strategies","volume":"118","author":"Bisola Bello","year":"2024","journal-title":"Pathogens and Global Health."},{"issue":"3","key":"10.1016\/j.mimet.2025.107268_bb0045","article-title":"Epithelial invasion by Salmonella typhi using STIV\u2013met interaction","volume":"21","author":"Chowdhury","year":"2019","journal-title":"Cell. Microbiol."},{"issue":"9","key":"10.1016\/j.mimet.2025.107268_bb0050","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1002\/pro.5560020916","article-title":"ERRAT: an empirical atom-based method for validating protein structures","volume":"2","author":"Colovos","year":"1993","journal-title":"Protein Sci."},{"issue":"3","key":"10.1016\/j.mimet.2025.107268_bb0055","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.imbio.2019.02.011","article-title":"Salmonella typhi outer membrane protein STIV is a potential candidate for vaccine development against typhoid and paratyphoid fever","volume":"224","author":"Das","year":"2019","journal-title":"Immunobiology"},{"issue":"1","key":"10.1016\/j.mimet.2025.107268_bb0060","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1471-2105-8-4","article-title":"VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines","volume":"8","author":"Doytchinova","year":"2007","journal-title":"BMC Bioinform."},{"issue":"4","key":"10.1016\/j.mimet.2025.107268_bb0065","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1002\/jmr.893","article-title":"Predicting linear B-cell epitopes using string kernels","volume":"21","author":"EL-Manzalawy Y, Dobbs D, Honavar V.","year":"2008","journal-title":"J. Mol. Recogn.: An Interdiscipl. J."},{"issue":"5","key":"10.1016\/j.mimet.2025.107268_bb0070","doi-asserted-by":"crossref","first-page":"3374","DOI":"10.1016\/j.ygeno.2020.06.022","article-title":"Identification of novel vaccine candidate against Salmonella enterica serovar typhi by reverse vaccinology method and evaluation of its immunization","volume":"112","author":"Esmailnia","year":"2020","journal-title":"Genomics"},{"key":"10.1016\/j.mimet.2025.107268_bb0075","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1016\/S0076-6879(96)66034-0","article-title":"[32] GOR method for predicting protein secondary structure from amino acid sequence","volume":"266","author":"Garnier","year":"1996","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.mimet.2025.107268_bb0080","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1385\/1-59259-890-0:571","article-title":"Protein identification and analysis tools on the ExPASy server","author":"Gasteiger","year":"2005","journal-title":"The proteomics protocols handbook."},{"issue":"7","key":"10.1016\/j.mimet.2025.107268_bb0085","doi-asserted-by":"crossref","first-page":"669","DOI":"10.2174\/092986607781483912","article-title":"Ramachandran plot on the web (2.0)","volume":"14","author":"Gopalakrishnan","year":"2007","journal-title":"Protein Pept. Lett."},{"issue":"16","key":"10.1016\/j.mimet.2025.107268_bb0090","doi-asserted-by":"crossref","first-page":"5315","DOI":"10.1021\/acs.jctc.3c00513","article-title":"Computational methods in immunology and vaccinology: design and development of antibodies and immunogens","volume":"19","author":"Guarra","year":"2023","journal-title":"J. Chem. Theory Comput."},{"issue":"2","key":"10.1016\/j.mimet.2025.107268_bb0095","first-page":"229","article-title":"Design and in silico analysis of pentavalent chimeric antigen against three enteropathogenic bacteria: enterotoxigenic E. Coli, enterohemorragic E. Coli and Shigella. Bioscience biotechnology research","volume":"9","author":"Hajizade","year":"2016","journal-title":"Communications"},{"issue":"19","key":"10.1016\/j.mimet.2025.107268_bb0100","doi-asserted-by":"crossref","first-page":"3098","DOI":"10.1093\/bioinformatics\/btx345","article-title":"Protein\u2013sol: a web tool for predicting protein solubility from sequence","volume":"33","author":"Hebditch","year":"2017","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/j.mimet.2025.107268_bb0105","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"10.1016\/j.mimet.2025.107268_bb0110","article-title":"Host restriction, pathogenesis and chronic carriage of typhoidal Salmonella","volume":"45(5):fuab014","author":"J. Barton A, Hill J, J. Blohmke C, J. Pollard A.","year":"2021","journal-title":"FEMS Microbiol. Rev."},{"issue":"10111","key":"10.1016\/j.mimet.2025.107268_bb0115","doi-asserted-by":"crossref","first-page":"2472","DOI":"10.1016\/S0140-6736(17)32149-9","article-title":"Efficacy and immunogenicity of a vi-tetanus toxoid conjugate vaccine in the prevention of typhoid fever using a controlled human infection model of Salmonella typhi: a randomised controlled, phase 2b trial","volume":"390","author":"Jin","year":"2017","journal-title":"Lancet"},{"issue":"8","key":"10.1016\/j.mimet.2025.107268_bb0125","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1038\/nprot.2012.085","article-title":"Template-based protein structure modeling using the RaptorX web server","volume":"7","author":"K\u00e4llberg","year":"2012","journal-title":"Nat. Protoc."},{"issue":"6","key":"10.1016\/j.mimet.2025.107268_bb0130","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.mimet.2025.107268_bb0135","first-page":"2.6","article-title":"Type 1 fimbriae, curli, and antigen 43: adhesion, colonization, and biofilm formation","volume":"1(1):10.1128\/ecosalplus. 8.3","author":"Klemm","year":"2004","journal-title":"EcoSal Plus"},{"issue":"2","key":"10.1016\/j.mimet.2025.107268_bb0140","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/nprot.2016.169","article-title":"The ClusPro web server for protein\u2013protein docking","volume":"12","author":"Kozakov","year":"2017","journal-title":"Nat. Protoc."},{"issue":"12","key":"10.1016\/j.mimet.2025.107268_bb0145","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1002829","article-title":"Reliable B cell epitope predictions: impacts of method development and improved benchmarking","volume":"8","author":"Kringelum","year":"2012","journal-title":"PLoS Comput. Biol."},{"issue":"11","key":"10.1016\/j.mimet.2025.107268_bb0150","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1016\/j.str.2003.10.002","article-title":"Protein disorder prediction: implications for structural proteomics","volume":"11","author":"Linding","year":"2003","journal-title":"Structure"},{"issue":"3","key":"10.1016\/j.mimet.2025.107268_bb0155","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1002\/prot.10286","article-title":"Structure validation by c\u03b1 geometry: \u03d5, \u03c8 and c\u03b2 deviation","volume":"50","author":"Lovell","year":"2003","journal-title":"Proteins: Struct., Funct., Bioinf."},{"key":"10.1016\/j.mimet.2025.107268_bb0160","article-title":"In silico vaccine design: A tutorial in immunoinformatics","volume":"2","author":"Martinelli","year":"2022","journal-title":"Healthcare Analyt."},{"key":"10.1016\/j.mimet.2025.107268_bb0165","article-title":"Multi-epitope vaccines, from design to expression; an in silico approach","volume":"110804","author":"Mortazavi","year":"2024","journal-title":"Hum. Immunol."},{"issue":"7","key":"10.1016\/j.mimet.2025.107268_bb0170","doi-asserted-by":"crossref","first-page":"5667","DOI":"10.1074\/jbc.M307759200","article-title":"Identification of conserved domains in Salmonella muenchen flagellin that are essential for its ability to activate TLR5 and to induce an inflammatory response in vitro","volume":"279","author":"Murthy","year":"2004","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.mimet.2025.107268_bb0175","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.molimm.2019.09.018","article-title":"Designing a multi-epitope vaccine for cross-protection against Shigella spp: an immunoinformatics and structural vaccinology study","volume":"116","author":"Nosrati","year":"2019","journal-title":"Mol. Immunol."},{"issue":"11","key":"10.1016\/j.mimet.2025.107268_bb0180","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.3390\/vaccines12111212","article-title":"Differential adjuvant activity by flagellins from Escherichia coli, Salmonella enterica serotype typhimurium, and Pseudomonas aeruginosa","volume":"12","author":"Pang","year":"2024","journal-title":"Vaccines"},{"key":"10.1016\/j.mimet.2025.107268_bb0200","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiomed.2024.108926","article-title":"ToxinPred 3.0: an improved method for predicting the toxicity of peptides","volume":"179","author":"Rathore","year":"2024","journal-title":"Comput. Biol. Med."},{"issue":"23","key":"10.1016\/j.mimet.2025.107268_bb0205","doi-asserted-by":"crossref","first-page":"8739","DOI":"10.1073\/pnas.0401283101","article-title":"Antigen selection based on expression levels during infection facilitates vaccine development for an intracellular pathogen","volume":"101","author":"Rollenhagen","year":"2004","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"1","key":"10.1016\/j.mimet.2025.107268_bb0210","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1002\/prot.21078","article-title":"Prediction of continuous B-cell epitopes in an antigen using recurrent neural network","volume":"65","author":"Saha","year":"2006","journal-title":"Proteins: Struct, Funct. Bioinform."},{"issue":"11","key":"10.1016\/j.mimet.2025.107268_bb0215","doi-asserted-by":"crossref","first-page":"7184","DOI":"10.4049\/jimmunol.180.11.7184","article-title":"Both radioresistant and hemopoietic cells promote innate and adaptive immune responses to flagellin","volume":"180","author":"Sanders","year":"2008","journal-title":"J. Immunol."},{"issue":"4","key":"10.1016\/j.mimet.2025.107268_bb0220","doi-asserted-by":"crossref","first-page":"501","DOI":"10.3390\/pharmaceutics13040501","article-title":"Rational vaccine design in times of emerging diseases: the critical choices of immunological correlates of protection, vaccine antigen and immunomodulation","volume":"13","author":"Schijns","year":"2021","journal-title":"Pharmaceutics"},{"key":"10.1016\/j.mimet.2025.107268_bb0225","article-title":"AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes","volume":"22(4):bbaa294","author":"Sharma","year":"2021","journal-title":"Brief. Bioinform."},{"issue":"4","key":"10.1016\/j.mimet.2025.107268_bb0230","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/S1473-3099(18)30685-6","article-title":"The global burden of typhoid and paratyphoid fevers: a systematic analysis for the global burden of disease study 2017","volume":"19","author":"Stanaway","year":"2019","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.mimet.2025.107268_bb0235","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2180-4-33","article-title":"Flagellin acting via TLR5 is the major activator of key signaling pathways leading to NF-\u03baB and proinflammatory gene program activation in intestinal epithelial cells","volume":"4","author":"Tallant","year":"2004","journal-title":"BMC Microbiol."},{"issue":"D1","key":"10.1016\/j.mimet.2025.107268_bb0240","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gky1006","article-title":"The immune epitope database (IEDB): 2018 update","volume":"47","author":"Vita","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mimet.2025.107268_bb0245","doi-asserted-by":"crossref","first-page":"1013159","DOI":"10.3389\/fimmu.2022.1013159","article-title":"Excretory\/secretory proteins inhibit host immune responses by downregulating the TLR4\/NF-\u03baB\/MAPKs signaling pathway: A possible mechanism of immune evasion in parasitic nematode Haemonchus contortus","volume":"13","author":"Wen","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.mimet.2025.107268_bb0250","article-title":"ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins","volume":"35(suppl_2):W407-W10","author":"Wiederstein","year":"2007","journal-title":"Nucleic Acids Res."},{"issue":"W1","key":"10.1016\/j.mimet.2025.107268_bb0255","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkv342","article-title":"I-TASSER server: new development for protein structure and function predictions","volume":"43","author":"Yang","year":"2015","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"10.1016\/j.mimet.2025.107268_bb0260","doi-asserted-by":"crossref","first-page":"45","DOI":"10.3390\/vaccines6030045","article-title":"Why is eradicating typhoid fever so challenging: implications for vaccine and therapeutic design","volume":"6","author":"Yang","year":"2018","journal-title":"Vaccines"},{"issue":"6070","key":"10.1016\/j.mimet.2025.107268_bb0265","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1126\/science.1215584","article-title":"Structural basis of TLR5-flagellin recognition and signaling","volume":"335","author":"Yoon","year":"2012","journal-title":"Science"}],"container-title":["Journal of Microbiological Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0167701225001848?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0167701225001848?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T04:01:59Z","timestamp":1761192119000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0167701225001848"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11]]},"references-count":48,"alternative-id":["S0167701225001848"],"URL":"https:\/\/doi.org\/10.1016\/j.mimet.2025.107268","relation":{},"ISSN":["0167-7012"],"issn-type":[{"value":"0167-7012","type":"print"}],"subject":[],"published":{"date-parts":[[2025,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Design and in silico evaluation of a novel chimeric protein vaccine candidate against Salmonella Typhi","name":"articletitle","label":"Article Title"},{"value":"Journal of Microbiological Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.mimet.2025.107268","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier B.V. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"107268"}}