{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T12:24:53Z","timestamp":1781785493272,"version":"3.54.5"},"reference-count":81,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T00:00:00Z","timestamp":1752537600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T00:00:00Z","timestamp":1752537600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Divers"],"published-print":{"date-parts":[[2026,2]]},"DOI":"10.1007\/s11030-025-11249-9","type":"journal-article","created":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T16:10:24Z","timestamp":1752595824000},"page":"1487-1505","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Immunoinformatics-driven design of a multi-epitope vaccine for effective protection against Machupo virus"],"prefix":"10.1007","volume":"30","author":[{"given":"Abdulaziz","family":"Alamri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saeedah","family":"Almutairi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salman","family":"Al Rokayan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed Y.","family":"Zaky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mostafa A.","family":"Abdel-Maksoud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Israr","family":"Fatima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,7,15]]},"reference":[{"issue":"1","key":"11249_CR1","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1146\/annurev-virology-101416-042001","volume":"4","author":"N Sarute","year":"2017","unstructured":"Sarute N, Ross SR (2017) New world arenavirus biology. Annu Rev Virol 4(1):141\u2013158","journal-title":"Annu Rev Virol"},{"key":"11249_CR2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tmaid.2021.102001","volume":"40","author":"CR Silva-Ramos","year":"2021","unstructured":"Silva-Ramos CR et al (2021) Bolivian hemorrhagic fever: a narrative review. Travel Med Infect Dis 40:102001","journal-title":"Travel Med Infect Dis"},{"key":"11249_CR3","unstructured":"Gonzalez J-P, Sauvage F (2013) Machupo, Guanarito, Sabia, and Chapare Viruses"},{"key":"11249_CR4","unstructured":"Ba L, et al (2010) Lassa, Junin, Machupo and Guanarito Viruses. Desk Encyclopedia"},{"issue":"3703","key":"11249_CR5","doi-asserted-by":"publisher","first-page":"1618","DOI":"10.1126\/science.150.3703.1618","volume":"150","author":"KM Johnson","year":"1965","unstructured":"Johnson KM et al (1965) Chronic infection of rodents by Machupo virus. Science 150(3703):1618\u20131619","journal-title":"Science"},{"issue":"5198","key":"11249_CR6","doi-asserted-by":"publisher","first-page":"1090","DOI":"10.1038\/2221090a0","volume":"222","author":"G Justines","year":"1969","unstructured":"Justines G, Johnson KM (1969) Immune tolerance in Calomys callosus infected with Machupo virus. Nature 222(5198):1090\u20131091","journal-title":"Nature"},{"issue":"1","key":"11249_CR7","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1177\/0300985815588609","volume":"53","author":"T Bell","year":"2016","unstructured":"Bell T et al (2016) Pathogenesis of Bolivian hemorrhagic fever in guinea pigs. Vet Pathol 53(1):190\u2013199","journal-title":"Vet Pathol"},{"key":"11249_CR8","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1016\/j.coviro.2014.02.007","volume":"5","author":"M Patterson","year":"2014","unstructured":"Patterson M, Grant A, Paessler S (2014) Epidemiology and pathogenesis of Bolivian hemorrhagic fever. Curr Opin Virol 5:82\u201390","journal-title":"Curr Opin Virol"},{"issue":"7800","key":"11249_CR9","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1038\/s41586-020-2114-2","volume":"579","author":"R Peng","year":"2020","unstructured":"Peng R et al (2020) Structural insight into arenavirus replication machinery. Nature 579(7800):615\u2013619","journal-title":"Nature"},{"issue":"46","key":"11249_CR10","doi-asserted-by":"publisher","first-page":"20069","DOI":"10.1073\/pnas.1007152107","volume":"107","author":"PJ Kranzusch","year":"2010","unstructured":"Kranzusch PJ et al (2010) Assembly of a functional Machupo virus polymerase complex. Proc Natl Acad Sci 107(46):20069\u201320074","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"11249_CR11","doi-asserted-by":"publisher","first-page":"4134","DOI":"10.1038\/s41467-021-24458-1","volume":"12","author":"H Kang","year":"2021","unstructured":"Kang H et al (2021) Structural basis for recognition and regulation of arenavirus polymerase L by Z protein. Nat Commun 12(1):4134","journal-title":"Nat Commun"},{"issue":"1","key":"11249_CR12","doi-asserted-by":"publisher","first-page":"6163","DOI":"10.1038\/s41467-021-26432-3","volume":"12","author":"J Ma","year":"2021","unstructured":"Ma J, Zhang S, Zhang X (2021) Structure of Machupo virus polymerase in complex with matrix protein Z. Nat Commun 12(1):6163","journal-title":"Nat Commun"},{"issue":"22","key":"11249_CR13","doi-asserted-by":"publisher","first-page":"12978","DOI":"10.1073\/pnas.2133782100","volume":"100","author":"M Perez","year":"2003","unstructured":"Perez M, Craven RC, de la Torre JC (2003) The small RING finger protein Z drives arenavirus budding: implications for antiviral strategies. Proc Natl Acad Sci 100(22):12978\u201312983","journal-title":"Proc Natl Acad Sci"},{"issue":"7","key":"11249_CR14","doi-asserted-by":"publisher","first-page":"784","DOI":"10.3390\/v12070784","volume":"12","author":"RJ Stott","year":"2020","unstructured":"Stott RJ, Strecker T, Foster TL (2020) Distinct molecular mechanisms of host immune response modulation by arenavirus NP and Z proteins. Viruses 12(7):784","journal-title":"Viruses"},{"issue":"3","key":"11249_CR15","doi-asserted-by":"publisher","first-page":"1290","DOI":"10.1128\/JVI.02615-15","volume":"90","author":"T Koma","year":"2016","unstructured":"Koma T et al (2016) Machupo virus expressing GPC of the Candid# 1 vaccine strain of Junin virus is highly attenuated and immunogenic. J Virol 90(3):1290\u20131297","journal-title":"J Virol"},{"issue":"7","key":"11249_CR16","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1517\/17460441.2012.687719","volume":"7","author":"SR Radoshitzky","year":"2012","unstructured":"Radoshitzky SR et al (2012) Drug discovery technologies and strategies for Machupo virus and other New World arenaviruses. Expert Opin Drug Discov 7(7):613\u2013632","journal-title":"Expert Opin Drug Discov"},{"issue":"14","key":"11249_CR17","doi-asserted-by":"publisher","first-page":"2949","DOI":"10.1016\/j.vaccine.2020.02.053","volume":"38","author":"DM Johnson","year":"2020","unstructured":"Johnson DM et al (2020) Bivalent Junin & Machupo experimental vaccine based on alphavirus RNA replicon vector. Vaccine 38(14):2949\u20132959","journal-title":"Vaccine"},{"issue":"5","key":"11249_CR18","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1016\/j.coviro.2013.05.020","volume":"3","author":"CM Byrd","year":"2013","unstructured":"Byrd CM, Grosenbach DW, Hruby DE (2013) Antiviral options for biodefense. Curr Opin Virol 3(5):537\u2013541","journal-title":"Curr Opin Virol"},{"key":"11249_CR19","doi-asserted-by":"crossref","unstructured":"Silva-Ramos CR, et al (2024) Endemic arenaviruses in Latin America. In: Emerging viruses in Latin America: contemporary virology, pp 85\u2013137","DOI":"10.1007\/978-3-031-68419-7_4"},{"issue":"4","key":"11249_CR20","doi-asserted-by":"publisher","first-page":"2137","DOI":"10.1007\/s12010-023-04604-9","volume":"196","author":"Z Ali","year":"2024","unstructured":"Ali Z et al (2024) A multi-epitope vaccine candidate against Bolivian hemorrhagic fever caused by Machupo virus. Appl Biochem Biotechnol 196(4):2137\u20132160","journal-title":"Appl Biochem Biotechnol"},{"issue":"3","key":"11249_CR21","doi-asserted-by":"publisher","first-page":"635","DOI":"10.3390\/vaccines11030635","volume":"11","author":"T Saito","year":"2023","unstructured":"Saito T et al (2023) Vaccine candidates against arenavirus infections. Vaccines 11(3):635","journal-title":"Vaccines"},{"key":"11249_CR22","doi-asserted-by":"crossref","unstructured":"Carrion R, et al (2012) Vaccine platforms to control arenaviral hemorrhagic fevers. J Vac Vaccin 3(7):1000160","DOI":"10.4172\/2157-7560.1000160"},{"key":"11249_CR23","doi-asserted-by":"crossref","unstructured":"Oli AN, et al (2020) Immunoinformatics and vaccine development: an overview. ImmunoTargets Ther 9:13\u201330","DOI":"10.2147\/ITT.S241064"},{"key":"11249_CR24","doi-asserted-by":"crossref","unstructured":"Rawat SS, et al (2023) Immunoinformatics approaches for vaccine design: a fast and secure strategy for successful vaccine development. Vaccines 11(2):221","DOI":"10.3390\/vaccines11020221"},{"issue":"4","key":"11249_CR25","first-page":"1","volume":"14","author":"Y-T Lo","year":"2013","unstructured":"Lo Y-T et al (2013) Prediction of conformational epitopes with the use of a knowledge-based energy function and geometrically related neighboring residue characteristics. BMC Bioinformatics 14(4):1\u201310","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"11249_CR26","doi-asserted-by":"publisher","first-page":"515","DOI":"10.3390\/vaccines2030515","volume":"2","author":"W Li","year":"2014","unstructured":"Li W et al (2014) Peptide vaccine: progress and challenges. Vaccines 2(3):515\u2013536","journal-title":"Vaccines"},{"issue":"10","key":"11249_CR27","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1016\/S1359-6446(03)02689-8","volume":"8","author":"M Mora","year":"2003","unstructured":"Mora M et al (2003) Reverse vaccinology. Drug Discov Today 8(10):459\u2013464","journal-title":"Drug Discov Today"},{"issue":"1","key":"11249_CR28","doi-asserted-by":"publisher","first-page":"11783","DOI":"10.1038\/s41598-024-61074-7","volume":"14","author":"NA Rani","year":"2024","unstructured":"Rani NA et al (2024) Development of multi epitope subunit vaccines against emerging carp viruses Cyprinid herpesvirus 1 and 3 using immunoinformatics approach. Sci Rep 14(1):11783","journal-title":"Sci Rep"},{"issue":"10","key":"11249_CR29","doi-asserted-by":"publisher","first-page":"1732","DOI":"10.3390\/vaccines10101732","volume":"10","author":"M Naveed","year":"2022","unstructured":"Naveed M et al (2022) Immunoinformatics approach to design multi-epitope-based vaccine against machupo virus taking viral nucleocapsid as a potential candidate. Vaccines 10(10):1732","journal-title":"Vaccines"},{"key":"11249_CR30","doi-asserted-by":"crossref","unstructured":"Consortium U (2019) UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 47(D1):D506\u2013D515","DOI":"10.1093\/nar\/gky1049"},{"issue":"D1","key":"11249_CR31","doi-asserted-by":"publisher","first-page":"D339","DOI":"10.1093\/nar\/gky1006","volume":"47","author":"R Vita","year":"2019","unstructured":"Vita R et al (2019) The immune epitope database (IEDB): 2018 update. Nucleic Acids Res 47(D1):D339\u2013D343","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"11249_CR32","doi-asserted-by":"publisher","first-page":"4836","DOI":"10.1038\/s41598-024-55372-3","volume":"14","author":"P Chao","year":"2024","unstructured":"Chao P et al (2024) Proteomics-based vaccine targets annotation and design of multi-epitope vaccine against antibiotic-resistant Streptococcus gallolyticus. Sci Rep 14(1):4836","journal-title":"Sci Rep"},{"key":"11249_CR33","doi-asserted-by":"crossref","unstructured":"Chao P, et al (2025) Pan-vaccinomics strategy for developing a universal multi-epitope vaccine against endocarditis-related pathogens. Front Immunol 16:1524128","DOI":"10.3389\/fimmu.2025.1524128"},{"key":"11249_CR34","doi-asserted-by":"crossref","unstructured":"EL\u2010Manzalawy Y, Dobbs D, Honavar V (2008) Predicting linear B\u2010cell epitopes using string kernels. J Mol Recogn An Interdiscipl J 21(4):243\u2013255","DOI":"10.1002\/jmr.893"},{"key":"11249_CR35","doi-asserted-by":"crossref","unstructured":"Saha S, Raghava GPS (2006) Prediction of continuous B\u2010cell epitopes in an antigen using recurrent neural network. Proteins Struct Funct Bioinform 65(1):40\u201348","DOI":"10.1002\/prot.21078"},{"issue":"1","key":"11249_CR36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-8-4","volume":"8","author":"IA Doytchinova","year":"2007","unstructured":"Doytchinova IA, Flower DR (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 8(1):1\u20137","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"11249_CR37","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0073957","volume":"8","author":"S Gupta","year":"2013","unstructured":"Gupta S et al (2013) In silico approach for predicting toxicity of peptides and proteins. PLoS ONE 8(9):e73957","journal-title":"PLoS ONE"},{"issue":"7","key":"11249_CR38","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1038\/nbt1215","volume":"24","author":"M Moutaftsi","year":"2006","unstructured":"Moutaftsi M et al (2006) A consensus epitope prediction approach identifies the breadth of murine T CD8+-cell responses to vaccinia virus. Nat Biotechnol 24(7):817\u2013819","journal-title":"Nat Biotechnol"},{"issue":"1","key":"11249_CR39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1745-6150-8-30","volume":"8","author":"SK Dhanda","year":"2013","unstructured":"Dhanda SK, Vir P, Raghava GP (2013) Designing of interferon-gamma inducing MHC class-II binders. Biol Direct 8(1):1\u201315","journal-title":"Biol Direct"},{"issue":"1","key":"11249_CR40","volume":"2013","author":"SK Dhanda","year":"2013","unstructured":"Dhanda SK et al (2013) Prediction of IL4 inducing peptides. J Immunol Res 2013(1):263952","journal-title":"J Immunol Res"},{"issue":"1","key":"11249_CR41","doi-asserted-by":"publisher","first-page":"42851","DOI":"10.1038\/srep42851","volume":"7","author":"G Nagpal","year":"2017","unstructured":"Nagpal G et al (2017) Computer-aided designing of immunosuppressive peptides based on IL-10 inducing potential. Sci Rep 7(1):42851","journal-title":"Sci Rep"},{"key":"11249_CR42","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2020.104186","volume":"80","author":"E Ong","year":"2020","unstructured":"Ong E, He Y, Yang Z (2020) Epitope promiscuity and population coverage of Mycobacterium tuberculosis protein antigens in current subunit vaccines under development. Infect Genet Evol 80:104186","journal-title":"Infect Genet Evol"},{"issue":"2","key":"11249_CR43","doi-asserted-by":"publisher","first-page":"74","DOI":"10.6026\/97320630012074","volume":"12","author":"VK Garg","year":"2016","unstructured":"Garg VK et al (2016) MFPPI\u2013multi FASTA ProtParam interface. Bioinformation 12(2):74","journal-title":"Bioinformation"},{"key":"11249_CR44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-8-4","volume":"8","author":"IA Doytchinova","year":"2007","unstructured":"Doytchinova IA, Flower DR (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 8:1\u20137","journal-title":"BMC Bioinformatics"},{"key":"11249_CR45","doi-asserted-by":"crossref","unstructured":"Vita R, et al (2015) The immune epitope database (IEDB) 3.0. Nucleic acids Res 43(D1):D405\u2013D412","DOI":"10.1093\/nar\/gku938"},{"key":"11249_CR46","doi-asserted-by":"crossref","unstructured":"Dimitrov I, et al (2014) AllerTOP v. 2\u2014a server for in silico prediction of allergens. J Mol Model 20:1\u20136","DOI":"10.1007\/s00894-014-2278-5"},{"issue":"17","key":"11249_CR47","doi-asserted-by":"publisher","first-page":"2200","DOI":"10.1093\/bioinformatics\/btp386","volume":"25","author":"CN Magnan","year":"2009","unstructured":"Magnan CN, Randall A, Baldi P (2009) SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics 25(17):2200\u20132207","journal-title":"Bioinformatics"},{"key":"11249_CR48","doi-asserted-by":"crossref","unstructured":"Buchan DW, et al (2024) Deep learning for the PSIPRED protein analysis workbench. Nucleic Acids Res 52(W1):W287\u2013W293","DOI":"10.1093\/nar\/gkae328"},{"key":"11249_CR49","doi-asserted-by":"crossref","unstructured":"Kim DE, Chivian D, Baker D (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32(suppl_2):W526\u2013W531","DOI":"10.1093\/nar\/gkh468"},{"issue":"W1","key":"11249_CR50","doi-asserted-by":"publisher","first-page":"W384","DOI":"10.1093\/nar\/gkt458","volume":"41","author":"L Heo","year":"2013","unstructured":"Heo L, Park H, Seok C (2013) GalaxyRefine: Protein structure refinement driven by side-chain repacking. Nucleic Acids Res 41(W1):W384\u2013W388","journal-title":"Nucleic Acids Res"},{"key":"11249_CR51","doi-asserted-by":"crossref","unstructured":"Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35(Web Server issue):W407\u2013W410","DOI":"10.1093\/nar\/gkm290"},{"issue":"4","key":"11249_CR52","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1002\/prot.20530","volume":"60","author":"RJ Anderson","year":"2005","unstructured":"Anderson RJ et al (2005) Main-chain conformational tendencies of amino acids. Proteins 60(4):679\u2013689","journal-title":"Proteins"},{"issue":"6","key":"11249_CR53","first-page":"2443","volume":"31","author":"I Arif","year":"2018","unstructured":"Arif I et al (2018) A computational structural analysis of functional attributes of hypodermin A and B proteins: a way forward for vaccine development. Pak J Pharm Sci 31(6):2443\u20132451","journal-title":"Pak J Pharm Sci"},{"issue":"1","key":"11249_CR54","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-9-514","volume":"9","author":"J Ponomarenko","year":"2008","unstructured":"Ponomarenko J et al (2008) ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 9(1):1\u20138","journal-title":"BMC Bioinformatics"},{"key":"11249_CR55","doi-asserted-by":"crossref","unstructured":"Craig DB, Dombkowski AA (2013) Disulfide by design 2.0: a web-based tool for disulfide engineering in proteins. BMC Bioinformatics 14(1):1\u20137","DOI":"10.1186\/1471-2105-14-346"},{"issue":"4","key":"11249_CR56","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009862","volume":"5","author":"N Rapin","year":"2010","unstructured":"Rapin N et al (2010) Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PLoS ONE 5(4):e9862","journal-title":"PLoS ONE"},{"key":"11249_CR57","doi-asserted-by":"crossref","unstructured":"Honorato RV, et al (2024) The HADDOCK2. 4 web server for integrative modeling of biomolecular complexes. Nat Protoc 19(11):3219\u20133241","DOI":"10.1038\/s41596-024-01011-0"},{"issue":"2","key":"11249_CR58","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1298","volume":"7","author":"S Yuan","year":"2017","unstructured":"Yuan S, Chan HS, Hu Z (2017) Using PyMOL as a platform for computational drug design. Wiley Interdiscipl Rev Comput Mol Sci 7(2):e1298","journal-title":"Wiley Interdiscipl Rev Comput Mol Sci"},{"key":"11249_CR59","doi-asserted-by":"crossref","unstructured":"Laskowski RA (2009) PDBsum new things. Nucleic Acids Res 37(suppl_1): D355\u2013D359","DOI":"10.1093\/nar\/gkn860"},{"key":"11249_CR60","doi-asserted-by":"crossref","unstructured":"Jorgensen WL, et al (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926\u2013935","DOI":"10.1063\/1.445869"},{"key":"11249_CR61","doi-asserted-by":"crossref","unstructured":"Qureshi KA, et al (2021) In vitro and in silico approaches for the antileishmanial activity evaluations of actinomycins isolated from novel Streptomyces smyrnaeus strain UKAQ_23. Antibiotics 10(8):887","DOI":"10.3390\/antibiotics10080887"},{"key":"11249_CR62","doi-asserted-by":"crossref","unstructured":"Hess B, et al (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18(12):1463\u20131472","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H"},{"issue":"1\u20133","key":"11249_CR63","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1080\/08927029108022142","volume":"6","author":"H Grubm\u00fcller","year":"1991","unstructured":"Grubm\u00fcller H et al (1991) Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol Simul 6(1\u20133):121\u2013142","journal-title":"Mol Simul"},{"issue":"19","key":"11249_CR64","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","author":"U Essmann","year":"1995","unstructured":"Essmann U et al (1995) A smooth particle mesh Ewald method. J Chem Phys 103(19):8577\u20138593","journal-title":"J Chem Phys"},{"key":"11249_CR65","doi-asserted-by":"crossref","unstructured":"Grant BJ, Skjaerven L, Yao XQ (2021) The Bio3D packages for structural bioinformatics. Protein Sci 30(1):20\u201330","DOI":"10.1002\/pro.3923"},{"key":"11249_CR66","doi-asserted-by":"crossref","unstructured":"Huang J, MacKerell Jr AD (2013) CHARMM36 all\u2010atom additive protein force field: validation based on comparison to NMR data. J Comput Chem 34(25):2135\u20132145.","DOI":"10.1002\/jcc.23354"},{"key":"11249_CR67","unstructured":"Siddharth R, Shankar M, Karthikeyan A (2019) An overview on \u201cGensmart\u201d\u2013A smart DNA construct design tool."},{"issue":"7","key":"11249_CR68","doi-asserted-by":"publisher","first-page":"2963","DOI":"10.1080\/07391102.2020.1850357","volume":"40","author":"VS Ayyagari","year":"2022","unstructured":"Ayyagari VS et al (2022) Design of a multi-epitope-based vaccine targeting M-protein of SARS-CoV2: an immunoinformatics approach. J Biomol Struct Dyn 40(7):2963\u20132977","journal-title":"J Biomol Struct Dyn"},{"issue":"1","key":"11249_CR69","doi-asserted-by":"publisher","first-page":"13321","DOI":"10.1038\/s41598-019-49354-z","volume":"9","author":"M Khan","year":"2019","unstructured":"Khan M et al (2019) Immunoinformatics approaches to explore Helicobacter pylori proteome (Virulence Factors) to design B and T cell multi-epitope subunit vaccine. Sci Rep 9(1):13321","journal-title":"Sci Rep"},{"key":"11249_CR70","doi-asserted-by":"publisher","first-page":"1116400","DOI":"10.3389\/fvets.2022.1116400","volume":"9","author":"I Gul","year":"2023","unstructured":"Gul I et al (2023) A multiepitope vaccine candidate against infectious bursal disease virus using immunoinformatics-based reverse vaccinology approach. Front Vet Sci 9:1116400","journal-title":"Front Vet Sci"},{"issue":"1","key":"11249_CR71","doi-asserted-by":"publisher","first-page":"5568546","DOI":"10.1155\/dth\/5568546","volume":"2025","author":"L Zhu","year":"2025","unstructured":"Zhu L et al (2025) Noncoding RNAs in atopic dermatitis: insight into inflammation and immune regulation. Dermatol Ther 2025(1):5568546","journal-title":"Dermatol Ther"},{"key":"11249_CR72","doi-asserted-by":"crossref","unstructured":"Luan F, et al (2025) Comprehensive pan-cancer analysis reveals NTN1 as an immune infiltrate risk factor and its potential prognostic value in SKCM. Sci Rep 15(1):3223","DOI":"10.1038\/s41598-025-85444-x"},{"issue":"10","key":"11249_CR73","doi-asserted-by":"publisher","first-page":"997","DOI":"10.3390\/biology10100997","volume":"10","author":"S Aslam","year":"2021","unstructured":"Aslam S et al (2021) Designing a multi-epitope vaccine against chlamydia trachomatis by employing integrated core proteomics, immuno-informatics and in silico approaches. Biology 10(10):997","journal-title":"Biology"},{"issue":"11","key":"11249_CR74","doi-asserted-by":"publisher","first-page":"1373","DOI":"10.3390\/vaccines9111373","volume":"9","author":"A Umar","year":"2021","unstructured":"Umar A et al (2021) Development of a candidate multi-epitope subunit vaccine against Klebsiella aerogenes: subtractive proteomics and immuno-informatics approach. Vaccines 9(11):1373","journal-title":"Vaccines"},{"key":"11249_CR75","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2021.104795","volume":"91","author":"M Mahmood","year":"2021","unstructured":"Mahmood M et al (2021) Rational design of multimeric based subunit vaccine against Mycoplasma pneumonia: subtractive proteomics with immunoinformatics framework. Infect Genet Evol 91:104795","journal-title":"Infect Genet Evol"},{"key":"11249_CR76","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.molimm.2019.04.030","volume":"112","author":"A Safavi","year":"2019","unstructured":"Safavi A et al (2019) In silico analysis of transmembrane protein 31 (TMEM31) antigen to design novel multiepitope peptide and DNA cancer vaccines against melanoma. Mol Immunol 112:93\u2013102","journal-title":"Mol Immunol"},{"issue":"48","key":"11249_CR77","doi-asserted-by":"publisher","first-page":"7612","DOI":"10.1016\/j.vaccine.2020.10.016","volume":"38","author":"A Safavi","year":"2020","unstructured":"Safavi A et al (2020) Exploring the out of sight antigens of SARS-CoV-2 to design a candidate multi-epitope vaccine by utilizing immunoinformatics approaches. Vaccine 38(48):7612\u20137628","journal-title":"Vaccine"},{"key":"11249_CR78","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1016\/j.meegid.2017.02.007","volume":"49","author":"B Meza","year":"2017","unstructured":"Meza B et al (2017) A novel design of a multi-antigenic, multistage and multi-epitope vaccine against Helicobacter pylori: an in silico approach. Infect Genet Evol 49:309\u2013317","journal-title":"Infect Genet Evol"},{"key":"11249_CR79","doi-asserted-by":"crossref","unstructured":"Li S, et al (2024) Modified lentiviral globin gene therapy for pediatric \u03b20\/\u03b20 transfusion-dependent \u03b2-thalassemia: a single-center, single-arm pilot trial. Cel Stem Cell 31(7):961\u2013973.e8","DOI":"10.1016\/j.stem.2024.04.021"},{"key":"11249_CR80","doi-asserted-by":"crossref","unstructured":"Li X-F, et al (2024) The association of post-embryo transfer SARS-CoV-2 infection with early pregnancy outcomes in in vitro fertilization: a prospective cohort study. Am J Obstetr Gynecol 230(4):436.e1\u2013436.e12","DOI":"10.1016\/j.ajog.2023.12.022"},{"issue":"1","key":"11249_CR81","doi-asserted-by":"publisher","first-page":"2408608","DOI":"10.1002\/advs.202408608","volume":"12","author":"W Lin","year":"2025","unstructured":"Lin W et al (2025) Programmable macrophage vesicle based bionic self-adjuvanting vaccine for immunization against Monkeypox virus. Adv Sci 12(1):2408608","journal-title":"Adv Sci"}],"container-title":["Molecular Diversity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-025-11249-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11030-025-11249-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-025-11249-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,22]],"date-time":"2026-02-22T17:03:09Z","timestamp":1771779789000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11030-025-11249-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,15]]},"references-count":81,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,2]]}},"alternative-id":["11249"],"URL":"https:\/\/doi.org\/10.1007\/s11030-025-11249-9","relation":{},"ISSN":["1381-1991","1573-501X"],"issn-type":[{"value":"1381-1991","type":"print"},{"value":"1573-501X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,15]]},"assertion":[{"value":"8 February 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 May 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 July 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}