{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T06:28:40Z","timestamp":1790663320253,"version":"4.1.0"},"reference-count":91,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100002383","name":"King Saud University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["International Immunopharmacology"],"published-print":{"date-parts":[[2024,5]]},"DOI":"10.1016\/j.intimp.2024.111952","type":"journal-article","created":{"date-parts":[[2024,3,30]],"date-time":"2024-03-30T10:23:19Z","timestamp":1711794199000},"page":"111952","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":20,"special_numbering":"C","title":["Decrypting the multi-genome data for chimeric vaccine designing against the antibiotic resistant Yersinia pestis"],"prefix":"10.1016","volume":"132","author":[{"given":"Asifa","family":"Sarfraz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sayyada","family":"Qurrat-Ul-Ain Fatima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Shehroz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iqra","family":"Ahmad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aqal","family":"Zaman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0106-3068","authenticated-orcid":false,"given":"Umar","family":"Nishan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Tayyab","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"family":"Sheheryar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arlindo Alencar","family":"Moura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Riaz","family":"Ullah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Essam A.","family":"Ali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6126-7102","authenticated-orcid":false,"given":"Mohibullah","family":"Shah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.intimp.2024.111952_b0005","doi-asserted-by":"crossref","DOI":"10.15212\/ZOONOSES-2022-0040","article-title":"Yersinia pestis and plague: some knowns and unknowns","volume":"3","author":"Yang","year":"2023","journal-title":"Zoonoses"},{"key":"10.1016\/j.intimp.2024.111952_b0010","first-page":"598","article-title":"Overview of Yersinia pestis metallophores: yersiniabactin and yersinopine","volume":"12","author":"Chaaban","year":"2023","journal-title":"Biology (Basel)"},{"key":"10.1016\/j.intimp.2024.111952_b0015","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41435-019-0065-0","article-title":"Yersinia pestis and plague: an updated view on evolution, virulence determinants, immune subversion, vaccination, and diagnostics","volume":"20","author":"Demeure","year":"2019","journal-title":"Genes Immun."},{"key":"10.1016\/j.intimp.2024.111952_b0020","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1146\/annurev-micro-090816-093521","article-title":"\u201cFleaing\u201d the plague: adaptations of Yersinia pestis to its insect vector that Lead to transmission","volume":"71","author":"Hinnebusch","year":"2017","journal-title":"Annu. Rev. Microbiol."},{"key":"10.1016\/j.intimp.2024.111952_b0025","doi-asserted-by":"crossref","unstructured":"W.W. Lathem, S.D. Crosby, V.L. Miller, W.E. Goldman, Progression of primary pneumonic plague: A mouse model of infection, pathology, and bacterial transcriptional activity, in: Proceedings of the National Academy of Sciences, 102, 2005, pp. 17786\u201317791, doi: 10.1073\/pnas.0506840102.","DOI":"10.1073\/pnas.0506840102"},{"key":"10.1016\/j.intimp.2024.111952_b0030","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.tim.2015.11.008","article-title":"Pneumonic plague: the darker side of Yersinia pestis","volume":"24","author":"Pechous","year":"2016","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.intimp.2024.111952_b0035","doi-asserted-by":"crossref","DOI":"10.1128\/CMR.00044-19","article-title":"Yersinia pestis: the natural history of plague","volume":"34","author":"Barbieri","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.intimp.2024.111952_b0040","first-page":"25","article-title":"Yersinia pestis: still a plague in the 21st century","volume":"17","author":"Josko","year":"2004","journal-title":"Clin. Lab. Sci."},{"key":"10.1016\/j.intimp.2024.111952_b0045","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1038\/ni1386","article-title":"Virulence factors of Yersinia pestis are overcome by a strong lipopolysaccharide response","volume":"7","author":"Montminy","year":"2006","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.intimp.2024.111952_b0050","unstructured":"R. Pollitzer, Plague, Geneva, 1954."},{"key":"10.1016\/j.intimp.2024.111952_b0055","doi-asserted-by":"crossref","DOI":"10.3201\/eid3002.230759","article-title":"Multiple introductions of Yersinia pestis during urban pneumonic plague epidemic, Madagascar, 2017","volume":"30","author":"Andrianaivoarimanana","year":"2024","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.intimp.2024.111952_b0060","doi-asserted-by":"crossref","first-page":"146","DOI":"10.3390\/microorganisms12010146","article-title":"The natural and clinical history of plague: from the ancient pandemics to modern insights","volume":"12","author":"Bennasar-Figueras","year":"2024","journal-title":"Microorganisms"},{"key":"10.1016\/j.intimp.2024.111952_b0065","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1056\/NEJM199709043371004","article-title":"Multidrug resistance in Yersinia pestis mediated by a transferable plasmid","volume":"337","author":"Galimand","year":"1997","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.intimp.2024.111952_b0070","doi-asserted-by":"crossref","first-page":"2623","DOI":"10.1128\/AAC.01374-10","article-title":"Comparative efficacies of candidate antibiotics against Yersinia pestis in an in vitro pharmacodynamic model","volume":"55","author":"Louie","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.intimp.2024.111952_b0075","article-title":"Complete protection against Yersinia pestis in BALB\/c mouse model elicited by immunization with inhalable formulations of rF1-V10 fusion protein via aerosolized intratracheal inoculation","volume":"13","author":"Zhang","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.intimp.2024.111952_b0080","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1586\/14760584.7.2.209","article-title":"Current challenges in the development of vaccines for pneumonic plague","volume":"7","author":"Smiley","year":"2008","journal-title":"Expert Rev. Vaccines"},{"key":"10.1016\/j.intimp.2024.111952_b0085","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2016.00602","article-title":"Plague vaccine development: current research and future trends","volume":"7","author":"Verma","year":"2016","journal-title":"Front. Immunol."},{"key":"10.1016\/j.intimp.2024.111952_b0090","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s41541-019-0105-9","article-title":"Plague vaccine: recent progress and prospects","volume":"4","author":"Sun","year":"2019","journal-title":"npj Vaccines"},{"key":"10.1016\/j.intimp.2024.111952_b0095","doi-asserted-by":"crossref","DOI":"10.1016\/j.ygeno.2022.110301","article-title":"An integrated in silico based subtractive genomics and reverse vaccinology approach for the identification of novel vaccine candidate and chimeric vaccine against XDR Salmonella typhi H58","volume":"114","author":"Khan","year":"2022","journal-title":"Genomics"},{"key":"10.1016\/j.intimp.2024.111952_b0100","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fgene.2021.564056","article-title":"Genome-based drug target identification in human pathogen streptococcus gallolyticus","volume":"12","author":"Qureshi","year":"2021","journal-title":"Front. Genet."},{"key":"10.1016\/j.intimp.2024.111952_b0105","first-page":"2778","article-title":"Genome-wide core proteome analysis of Brucella melitensis strains for potential drug target prediction, mini-reviews in medicinal","volume":"21","author":"Rahman","year":"2020","journal-title":"Chemistry"},{"key":"10.1016\/j.intimp.2024.111952_b0110","doi-asserted-by":"crossref","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022, A general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.intimp.2024.111952_b0115","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1093\/nar\/gkt1131","article-title":"DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements","volume":"42","author":"Luo","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.intimp.2024.111952_b0120","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiomed.2021.104701","article-title":"Chlamydia trachomatis core genome data mining for promising novel drug targets and chimeric vaccine candidates identification","volume":"136","author":"Aslam","year":"2021","journal-title":"Comput. Biol. Med."},{"key":"10.1016\/j.intimp.2024.111952_b0125","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/s10989-020-10076-w","article-title":"Delineating novel therapeutic drug and vaccine targets for staphylococcus cornubiensis NW1T through computational analysis","volume":"27","author":"Shah","year":"2021","journal-title":"Int. J. Pept. Res. Ther."},{"key":"10.1016\/j.intimp.2024.111952_b0130","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.ygeno.2013.04.011","article-title":"Putative drug and vaccine target protein identification using comparative genomic analysis of KEGG annotated metabolic pathways of Mycoplasma hyopneumoniae","volume":"102","author":"Damte","year":"2013","journal-title":"Genomics"},{"key":"10.1016\/j.intimp.2024.111952_b0135","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.micpath.2018.09.033","article-title":"Reverse vaccinology and subtractive genomics-based putative vaccine targets identification for Burkholderia pseudomallei Bp1651","volume":"125","author":"Hizbullah","year":"2018","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.intimp.2024.111952_b0140","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1093\/bioinformatics\/btq249","article-title":"PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.intimp.2024.111952_b0145","doi-asserted-by":"crossref","first-page":"1402","DOI":"10.1110\/ps.03479604","article-title":"Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n -peptide compositions","volume":"13","author":"Yu","year":"2004","journal-title":"Protein Sci."},{"key":"10.1016\/j.intimp.2024.111952_b0150","doi-asserted-by":"crossref","first-page":"W459","DOI":"10.1093\/nar\/gky320","article-title":"BUSCA: an integrative web server to predict subcellular localization of proteins","volume":"46","author":"Savojardo","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.intimp.2024.111952_b0155","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2023.1259612","article-title":"Vaccinomics-based next-generation multi-epitope chimeric vaccine models prediction against Leishmania tropica - a hierarchical subtractive proteomics and immunoinformatics approach","volume":"14","author":"Aiman","year":"2023","journal-title":"Front. Immunol."},{"key":"10.1016\/j.intimp.2024.111952_b0160","doi-asserted-by":"crossref","first-page":"1","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 Bioinf."},{"key":"10.1016\/j.intimp.2024.111952_b0165","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00894-014-2278-5","article-title":"AllerTOP vol 2 - a server for in silico prediction of allergens","volume":"20","author":"Dimitrov","year":"2014","journal-title":"J. Mol. Model."},{"key":"10.1016\/j.intimp.2024.111952_b0170","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.intimp.2024.111952_b0175","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1006\/cbir.1999.0355","article-title":"Protein identification and analysis tools in the ExPASy server","volume":"23","author":"Cash","year":"1999","journal-title":"Cell Biol. Int."},{"key":"10.1016\/j.intimp.2024.111952_b0180","first-page":"1","article-title":"Structural informatics approach for designing an epitope-based vaccine against the brain-eating Naegleria fowleri","volume":"14","author":"Sarfraz","year":"2023","journal-title":"Front. Immunol."},{"key":"10.1016\/j.intimp.2024.111952_b0185","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiomed.2024.108056","article-title":"Immunoinformatics-driven in silico vaccine design for Nipah virus (NPV): integrating machine learning and computational epitope prediction","volume":"170","author":"Shahab","year":"2024","journal-title":"Comput. Biol. Med."},{"key":"10.1016\/j.intimp.2024.111952_b0190","doi-asserted-by":"crossref","first-page":"43341","DOI":"10.1021\/acsomega.3c07866","article-title":"Deciphering the immunogenicity of monkeypox proteins for designing the potential mRNA vaccine","volume":"8","author":"Shah","year":"2023","journal-title":"ACS Omega"},{"key":"10.1016\/j.intimp.2024.111952_b0195","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0073957","article-title":"In silico approach for predicting toxicity of peptides and proteins","volume":"8","author":"Gupta","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.intimp.2024.111952_b0200","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-9-62","article-title":"VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens","volume":"9","author":"Garg","year":"2008","journal-title":"BMC Bioinf."},{"issue":"2020","key":"10.1016\/j.intimp.2024.111952_b0205","first-page":"497","article-title":"Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China","volume":"395","author":"Huang","year":"2019","journal-title":"The Lancet"},{"key":"10.1016\/j.intimp.2024.111952_b0210","doi-asserted-by":"crossref","DOI":"10.1155\/2013\/263952","article-title":"Prediction of IL4 inducing peptides","volume":"2013","author":"Dhanda","year":"2013","journal-title":"Clin. Dev. Immunol."},{"key":"10.1016\/j.intimp.2024.111952_b0215","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1745-6150-8-30","article-title":"Designing of interferon-gamma inducing MHC class-II binders","volume":"8","author":"Dhanda","year":"2013","journal-title":"Biol. Direct"},{"key":"10.1016\/j.intimp.2024.111952_b0220","first-page":"1","article-title":"Immunoinformatic-guided novel mRNA vaccine designing to elicit immunogenic responses against the endemic Monkeypox virus","author":"Aiman","year":"2023","journal-title":"J. Biomol. Struct. Dyn."},{"key":"10.1016\/j.intimp.2024.111952_b0225","doi-asserted-by":"crossref","first-page":"430","DOI":"10.3390\/bioengineering10040430","article-title":"Annotation of potential vaccine targets and designing of mRNA-based multi-epitope vaccine against lumpy skin disease virus via reverse vaccinology and agent-based modeling","volume":"10","author":"Kakakhel","year":"2023","journal-title":"Bioengineering"},{"key":"10.1016\/j.intimp.2024.111952_b0230","doi-asserted-by":"crossref","first-page":"e0289773","DOI":"10.1371\/journal.pone.0289773","article-title":"Vaccinomics-aided next-generation novel multi-epitope-based vaccine engineering against multidrug resistant Shigella Sonnei: immunoinformatics and chemoinformatics approaches","volume":"18","author":"Aiman","year":"2023","journal-title":"PLoS One"},{"key":"10.1016\/j.intimp.2024.111952_b0235","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/07391102.2023.2293266","article-title":"Designing a novel chimeric multi-epitope vaccine subunit against Staphylococcus argenteus through artificial intelligence approach integrating pan-genome analysis, in vitro identification, and immunogenicity profiling","author":"Naveed","year":"2023","journal-title":"J. Biomol. Struct. Dyn."},{"key":"10.1016\/j.intimp.2024.111952_b0240","doi-asserted-by":"crossref","first-page":"2200","DOI":"10.1093\/bioinformatics\/btp386","article-title":"SOLpro: accurate sequence-based prediction of protein solubility","volume":"25","author":"Magnan","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.intimp.2024.111952_b0245","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1093\/bioinformatics\/11.6.681","article-title":"Sopma: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments","volume":"11","author":"Geourjon","year":"1995","journal-title":"Bioinformatics"},{"key":"10.1016\/j.intimp.2024.111952_b0250","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1093\/bioinformatics\/16.4.404","article-title":"The PSIPRED protein structure prediction server","volume":"16","author":"McGuffin","year":"2000","journal-title":"Bioinformatics"},{"key":"10.1016\/j.intimp.2024.111952_b0255","doi-asserted-by":"crossref","first-page":"W296","DOI":"10.1093\/nar\/gky427","article-title":"SWISS-MODEL: homology modelling of protein structures and complexes","volume":"46","author":"Waterhouse","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.intimp.2024.111952_b0260","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1093\/nar\/gkt458","article-title":"GalaxyRefine: protein structure refinement driven by side-chain repacking","volume":"41","author":"Heo","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.intimp.2024.111952_b0265","doi-asserted-by":"crossref","unstructured":"R.A. Laskowski, N. Furnham, J.M. Thornton, The Ramachandran plot and protein structure validation, Biomolecular Forms and Functions: A Celebration of 50 Years of the Ramachandran Map (2012) 62\u201375, doi: 10.1142\/9789814449144_0005.","DOI":"10.1142\/9789814449144_0005"},{"key":"10.1016\/j.intimp.2024.111952_b0270","doi-asserted-by":"crossref","unstructured":"C. Colovos, T. Yeates, Verification of protein structures: Patterns of nonbonded atomic interactions, (1993) 1511\u20131519.","DOI":"10.1002\/pro.5560020916"},{"key":"10.1016\/j.intimp.2024.111952_b0275","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/nprot.2016.169","article-title":"The ClusPro web server for protein-protein docking","volume":"12","author":"Kozakov","year":"2017","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.intimp.2024.111952_b0280","doi-asserted-by":"crossref","unstructured":"K.J. Bowers, D.E. Chow, H. Xu, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossvary, M.A. Moraes, F.D. Sacerdoti, J.K. Salmon, Y. Shan, D.E. Shaw, Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters, in: ACM\/IEEE SC 2006 Conference (SC\u201906), IEEE, 2006, pp. 43\u201343. Doi: 10.1109\/SC.2006.54.","DOI":"10.1109\/SC.2006.54"},{"key":"10.1016\/j.intimp.2024.111952_b0285","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s10822-013-9644-8","article-title":"Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments","volume":"27","author":"Madhavi Sastry","year":"2013","journal-title":"J. Comput. Aided Mol. Des."},{"key":"10.1016\/j.intimp.2024.111952_b0290","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1016\/j.tibs.2019.06.004","article-title":"Bringing molecular dynamics simulation data into view","volume":"44","author":"Hildebrand","year":"2019","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.intimp.2024.111952_b0295","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.intimp.2024.111952_b0300","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1080\/07391102.2014.931825","article-title":"Molecular simulation of N-acetylneuraminic acid analogs and molecular dynamics studies of cholera toxin-Neu5Gc complex","volume":"33","author":"Blessy","year":"2015","journal-title":"J. Biomol. Struct. Dyn."},{"key":"10.1016\/j.intimp.2024.111952_b0305","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1103\/PhysRevA.31.1695","article-title":"Canonical dynamics: equilibrium phase-space distributions","volume":"31","author":"Hoover","year":"1985","journal-title":"Phys. Rev. A (coll Park)"},{"key":"10.1016\/j.intimp.2024.111952_b0310","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-9-514","article-title":"ElliPro: a new structure-based tool for the prediction of antibody epitopes","volume":"9","author":"Ponomarenko","year":"2008","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.intimp.2024.111952_b0315","first-page":"1","article-title":"C-immsim: playing with the immune response","author":"Castiglione","year":"2004","journal-title":"Proceedings of the Sixteenth"},{"key":"10.1016\/j.intimp.2024.111952_b0320","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/nar\/gki376","article-title":"JCat: a novel tool to adapt codon usage of a target gene to its potential expression host","volume":"33","author":"Grote","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.intimp.2024.111952_b0325","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1128\/iai.53.2.272-277.1986","article-title":"Molecular cloning and expression in Escherichia coli K-12 of the O antigens of the Inaba and Ogawa serotypes of the Vibrio cholerae O1 lipopolysaccharides and their potential for vaccine development","volume":"53","author":"Manning","year":"1986","journal-title":"Infect. Immun."},{"key":"10.1016\/j.intimp.2024.111952_b0330","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10989-021-10356-z","article-title":"Molecular characterization and designing of a novel multiepitope vaccine construct against Pseudomonas aeruginosa","volume":"28","author":"Dey","year":"2022","journal-title":"Int. J. Pept. Res. Ther."},{"key":"10.1016\/j.intimp.2024.111952_b0335","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/j.jmgm.2018.01.010","article-title":"Immuno-informatics driven proteome-wide investigation revealed novel peptide-based vaccine targets against emerging multiple drug resistant Providencia stuartii","volume":"80","author":"Asad","year":"2018","journal-title":"J. Mol. Graph. Model."},{"key":"10.1016\/j.intimp.2024.111952_b0340","doi-asserted-by":"crossref","unstructured":"A. Rehman, S. Ahmad, F. Shahid, A. Albutti, A.S.S. Alwashmi, M.A. Aljasir, N. Alhumeed, M. Qasim, U.A. Ashfaq, M. Tahir ul Qamar, Integrated Core Proteomics, Subtractive Proteomics, and Immunoinformatics Investigation to Unveil a Potential Multi-Epitope Vaccine against Schistosomiasis, Vaccines (Basel) 9 (2021) 658. Doi: 10.3390\/vaccines9060658.","DOI":"10.3390\/vaccines9060658"},{"key":"10.1016\/j.intimp.2024.111952_b0345","doi-asserted-by":"crossref","unstructured":"A.M. Gouda, M.A. Soltan, K. Abd-elghany, A.E. Sileem, H.M. Elnahas, M.A. Ateya, M.H. Elbatreek, K.M. Darwish, H.A. Bogari, M.O. Lashkar, M.M. Aldurdunji, Integration of immunoinformatics and cheminformatics to design and evaluate a multitope vaccine against Klebsiella pneumoniae and Pseudomonas aeruginosa coinfection, (2023) 1\u201322. Doi: 10.3389\/fmolb.2023.1123411.","DOI":"10.3389\/fmolb.2023.1123411"},{"key":"10.1016\/j.intimp.2024.111952_b0350","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fmicb.2022.971263","article-title":"Multi-epitope chimeric vaccine designing and novel drug targets prioritization against multi-drug resistant Staphylococcus pseudintermedius","volume":"13","author":"Jaan","year":"2022","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.intimp.2024.111952_b0355","doi-asserted-by":"crossref","first-page":"1017315","DOI":"10.3389\/fcimb.2023.1017315","article-title":"Computer-aided genomic data analysis of drug-resistant Neisseria gonorrhoeae for the identification of alternative therapeutic targets","volume":"13","author":"Qasim","year":"2023","journal-title":"Front. Cell. Infect. Microbiol."},{"issue":"1995","key":"10.1016\/j.intimp.2024.111952_b0360","first-page":"720","article-title":"Generation of memory B cells and plasma cells in vitro","volume":"268","author":"Arpin","year":"1979","journal-title":"Science"},{"key":"10.1016\/j.intimp.2024.111952_b0365","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/j.autrev.2005.04.005","article-title":"CD4+ regulatory T cells: mechanisms of induction and effector function","volume":"4","author":"Bacchetta","year":"2005","journal-title":"Autoimmun. Rev."},{"key":"10.1016\/j.intimp.2024.111952_b0370","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/s41598-021-03990-6","article-title":"In silico construction of a multiepitope Zika virus vaccine using immunoinformatics tools","volume":"12","author":"Antonelli","year":"2022","journal-title":"Sci. Rep."},{"key":"10.1016\/j.intimp.2024.111952_b0375","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.fsi.2022.03.017","article-title":"\u03b2-Defensin: an adroit saviour in teleosts","volume":"123","author":"Das","year":"2022","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.intimp.2024.111952_b0380","doi-asserted-by":"crossref","first-page":"60035","DOI":"10.1007\/s11356-022-19979-1","article-title":"Reverse vaccinology approach for multi-epitope centered vaccine design against delta variant of the SARS-CoV-2","volume":"29","author":"Jalal","year":"2022","journal-title":"Environ. Sci. Pollut. Res."},{"key":"10.1016\/j.intimp.2024.111952_b0385","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijmm.2021.151508","article-title":"Reverse vaccinology approach for the identifications of potential vaccine candidates against Salmonella","volume":"311","author":"Li","year":"2021","journal-title":"Int. J. Med. Microbiol."},{"key":"10.1016\/j.intimp.2024.111952_b0390","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/j.ygeno.2018.02.017","article-title":"A comparative in silico linear B-cell epitope prediction and characterization for South American and African Trypanosoma vivax strains","volume":"111","author":"Guedes","year":"2019","journal-title":"Genomics"},{"key":"10.1016\/j.intimp.2024.111952_b0395","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.meegid.2019.03.003","article-title":"Vaccinomics strategy for developing a unique multi-epitope monovalent vaccine against Marburg marburgvirus","volume":"70","author":"Hasan","year":"2019","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.intimp.2024.111952_b0400","doi-asserted-by":"crossref","first-page":"34","DOI":"10.3390\/vaccines7020034","article-title":"In silico designed ebola virus T-cell multi-epitope DNA vaccine constructions are immunogenic in mice","volume":"7","author":"Bazhan","year":"2019","journal-title":"Vaccines (Basel)"},{"key":"10.1016\/j.intimp.2024.111952_b0405","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.706510","article-title":"Blockade of TLR2 and TLR4 attenuates inflammatory response and parasite load in cutaneous leishmaniasis","volume":"12","author":"Carneiro","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.intimp.2024.111952_b0410","article-title":"Design and immunological evaluation of a hybrid peptide as a potent TLR2 agonist by structure-based virtual screening","volume":"9","author":"Zhang","year":"2021","journal-title":"Front. Cell Dev. Biol."},{"key":"10.1016\/j.intimp.2024.111952_b0415","doi-asserted-by":"crossref","first-page":"627","DOI":"10.3390\/molecules25030627","article-title":"TLR4-targeting therapeutics: structural basis and computer-aided drug discovery approaches","volume":"25","author":"ul Ain","year":"2020","journal-title":"Molecules"},{"key":"10.1016\/j.intimp.2024.111952_b0420","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.998262","article-title":"In-silico evaluation of adenoviral COVID-19 vaccination protocols: assessment of immunological memory up to 6 months after the third dose","volume":"13","author":"Stolfi","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.intimp.2024.111952_b0425","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.ejca.2018.12.022","article-title":"Safety of trastuzumab emtansine (T-DM1) in patients with HER2-positive advanced breast cancer: primary results from the KAMILLA study cohort 1","volume":"109","author":"Montemurro","year":"2019","journal-title":"Eur. J. Cancer"},{"key":"10.1016\/j.intimp.2024.111952_b0430","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.3390\/vaccines9111327","article-title":"Annotation of potential vaccine targets and design of a multi-epitope subunit vaccine against Yersinia pestis through reverse vaccinology and validation through an agent-based modeling approach","volume":"9","author":"Haq","year":"2021","journal-title":"Vaccines (Basel)"},{"key":"10.1016\/j.intimp.2024.111952_b0435","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.3390\/ph16081124","article-title":"Identification of drug targets and their inhibitors in Yersinia pestis Strain 91001 through subtractive genomics, machine learning, and md simulation approaches","volume":"16","author":"Ali","year":"2023","journal-title":"Pharmaceuticals"},{"key":"10.1016\/j.intimp.2024.111952_b0440","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiolchem.2022.107784","article-title":"In-silico approach of identifying novel therapeutic targets against Yersinia pestis using pan and subtractive genomic analysis","volume":"101","author":"Islam","year":"2022","journal-title":"Comput. Biol. Chem."},{"key":"10.1016\/j.intimp.2024.111952_b0445","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.ejmech.2012.09.018","article-title":"Identification of potential drug targets in Yersinia pestis using metabolic pathway analysis: MurE ligase as a case study","volume":"57","author":"Sharma","year":"2012","journal-title":"Eur. J. Med. Chem."},{"key":"10.1016\/j.intimp.2024.111952_b0450","doi-asserted-by":"crossref","DOI":"10.1016\/j.intimp.2023.110725","article-title":"Immunoinformatics-based multi-epitope vaccine design for the re-emerging monkeypox virus","volume":"123","author":"Farzan","year":"2023","journal-title":"Int. Immunopharmacol."},{"key":"10.1016\/j.intimp.2024.111952_b0455","doi-asserted-by":"crossref","first-page":"1734","DOI":"10.1016\/j.ygeno.2019.10.009","article-title":"Potential druggable proteins and chimeric vaccine construct prioritization against Brucella melitensis from species core genome data","volume":"112","author":"Aslam","year":"2020","journal-title":"Genomics"}],"container-title":["International Immunopharmacology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1567576924004703?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1567576924004703?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,11,15]],"date-time":"2024-11-15T09:29:07Z","timestamp":1731662947000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1567576924004703"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5]]},"references-count":91,"alternative-id":["S1567576924004703"],"URL":"https:\/\/doi.org\/10.1016\/j.intimp.2024.111952","relation":{},"ISSN":["1567-5769"],"issn-type":[{"value":"1567-5769","type":"print"}],"subject":[],"published":{"date-parts":[[2024,5]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Decrypting the multi-genome data for chimeric vaccine designing against the antibiotic resistant Yersinia pestis","name":"articletitle","label":"Article Title"},{"value":"International Immunopharmacology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.intimp.2024.111952","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"111952"}}