{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,14]],"date-time":"2024-08-14T00:24:09Z","timestamp":1723595049771},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"8","license":[{"start":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T00:00:00Z","timestamp":1722384000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T00:00:00Z","timestamp":1722384000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"National post-doctoral fellowship, DST-SERB, Govt. of India","award":["PDF\/2018-002631"],"award-info":[{"award-number":["PDF\/2018-002631"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Mol Model"],"published-print":{"date-parts":[[2024,8]]},"DOI":"10.1007\/s00894-024-06088-8","type":"journal-article","created":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T11:14:16Z","timestamp":1722424456000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Predicting immune response targets in orthoflaviviruses through sequence homology and computational analysis"],"prefix":"10.1007","volume":"30","author":[{"given":"Venkata N.","family":"Are","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajarshi","family":"Roy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandeep Kumar","family":"Dhanda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sanchit","family":"Neema","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neha Rani","family":"Sahu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nitin","family":"Adithya","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ritudhwaj","family":"Tiwari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Parimal","family":"Kar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Debasis","family":"Nayak","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,7,31]]},"reference":[{"key":"6088_CR1","doi-asserted-by":"publisher","first-page":"149","DOI":"10.3389\/fcimb.2018.00149","volume":"8","author":"SZ Shah","year":"2018","unstructured":"Shah SZ, Jabbar B, Ahmed N et al (2018) Epidemiology, pathogenesis, and control of a tick-borne disease- Kyasanur forest disease: current status and future directions. Front Cell Infect Microbiol 8:149. https:\/\/doi.org\/10.3389\/fcimb.2018.00149","journal-title":"Front Cell Infect Microbiol"},{"key":"6088_CR2","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1002\/rmv.580","volume":"18","author":"P Pattnaik","year":"2008","unstructured":"Pattnaik P (2008) Kyasanur forest disease: an epidemiological view in India. Rev Med Virol 18:211\u2013211. https:\/\/doi.org\/10.1002\/rmv.580","journal-title":"Rev Med Virol"},{"key":"6088_CR3","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1186\/s40249-015-0066-9","volume":"4","author":"MV Murhekar","year":"2015","unstructured":"Murhekar MV, Kasabi GS, Mehendale SM et al (2015) On the transmission pattern of Kyasanur Forest disease (KFD) in India. Infect Dis Poverty 4:37. https:\/\/doi.org\/10.1186\/s40249-015-0066-9","journal-title":"Infect Dis Poverty"},{"key":"6088_CR4","doi-asserted-by":"publisher","DOI":"10.3201\/eid1612101092","author":"F Carletti","year":"2010","unstructured":"Carletti F (2010) Alkhurma hemorrhagic fever in travelers returning from Egypt, 2010. Emerg Infect Dis. https:\/\/doi.org\/10.3201\/eid1612101092","journal-title":"Emerg Infect Dis"},{"key":"6088_CR5","doi-asserted-by":"publisher","first-page":"e100301","DOI":"10.1371\/journal.pone.0100301","volume":"9","author":"KA Dodd","year":"2014","unstructured":"Dodd KA, Bird BH, Jones MEB et al (2014) Kyasanur forest disease virus infection in mice is associated with higher morbidity and mortality than infection with the closely related Alkhurma hemorrhagic fever virus. PLoS ONE 9:e100301. https:\/\/doi.org\/10.1371\/journal.pone.0100301","journal-title":"PLoS ONE"},{"key":"6088_CR6","unstructured":"Lindenbach BD, Rice CM (2007) Flaviviridae: the viruses and their replication. Fields Virol 1101\u201351"},{"key":"6088_CR7","doi-asserted-by":"publisher","first-page":"869","DOI":"10.2105\/AJPH.49.7.869","volume":"49","author":"TH Work","year":"1959","unstructured":"Work TH, Roderiguez FR, Bhatt PN (1959) Virological epidemiology of the 1958 epidemic of Kyasanur forest disease. Am J Public Health Nations Health 49:869\u2013874. https:\/\/doi.org\/10.2105\/AJPH.49.7.869","journal-title":"Am J Public Health Nations Health"},{"key":"6088_CR8","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1016\/j.antiviral.2012.10.005","volume":"96","author":"MR Holbrook","year":"2012","unstructured":"Holbrook MR (2012) Kyasanur forest disease. Antiviral Res 96:353\u2013362. https:\/\/doi.org\/10.1016\/j.antiviral.2012.10.005","journal-title":"Antiviral Res"},{"key":"6088_CR9","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.meegid.2019.02.012","volume":"70","author":"ul-Rahman A,","year":"2019","unstructured":"ul-Rahman A, (2019) Genetic diversity of Alkhurma hemorrhagic fever virus in Western Asia. Infect Genet Evol 70:80\u201383. https:\/\/doi.org\/10.1016\/j.meegid.2019.02.012","journal-title":"Infect Genet Evol"},{"key":"6088_CR10","doi-asserted-by":"publisher","first-page":"430","DOI":"10.12998\/wjcc.v3.i5.430","volume":"3","author":"P Bogovic","year":"2015","unstructured":"Bogovic P (2015) Tick-borne encephalitis: a review of epidemiology, clinical characteristics, and management. World J Clin Cases 3:430. https:\/\/doi.org\/10.12998\/wjcc.v3.i5.430","journal-title":"World J Clin Cases"},{"issue":"4","key":"6088_CR11","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/JCM.01783-19","volume":"58","author":"P Girl","year":"2020","unstructured":"Girl P, Bestehorn-Willmann M, Zange S et al (2020) Tick-borne encephalitis virus nonstructural protein 1 IgG enzyme-linked immunosorbent assay for differentiating infection versus vaccination antibody responses. J Clin Microbiol 58(4):10\u2013128. https:\/\/doi.org\/10.1128\/JCM.01783-19","journal-title":"J Clin Microbiol"},{"key":"6088_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ejim.2019.01.004","volume":"62","author":"N Riccardi","year":"2019","unstructured":"Riccardi N, Antonello RM, Luzzati R et al (2019) Tick-borne encephalitis in Europe: a brief update on epidemiology, diagnosis, prevention, and treatment. Eur J Intern Med 62:1\u20136. https:\/\/doi.org\/10.1016\/j.ejim.2019.01.004","journal-title":"Eur J Intern Med"},{"key":"6088_CR13","doi-asserted-by":"publisher","first-page":"4","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 8:4. https:\/\/doi.org\/10.1186\/1471-2105-8-4","journal-title":"BMC Bioinformatics"},{"key":"6088_CR14","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1093\/bioinformatics\/btv639","volume":"32","author":"M Andreatta","year":"2016","unstructured":"Andreatta M, Nielsen M (2016) Gapped sequence alignment using artificial neural networks: application to the MHC class I system. Bioinformatics 32:511\u2013517. https:\/\/doi.org\/10.1093\/bioinformatics\/btv639","journal-title":"Bioinformatics"},{"key":"6088_CR15","doi-asserted-by":"publisher","first-page":"2304","DOI":"10.1021\/acs.jproteome.9b00874","volume":"19","author":"B Reynisson","year":"2020","unstructured":"Reynisson B, Barra C, Kaabinejadian S et al (2020) Improved prediction of MHC II antigen presentation through integration and motif deconvolution of mass spectrometry MHC eluted ligand data. J Proteome Res 19:2304\u20132315. https:\/\/doi.org\/10.1021\/acs.jproteome.9b00874","journal-title":"J Proteome Res"},{"key":"6088_CR16","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1111\/imm.12984","volume":"155","author":"SK Dhanda","year":"2018","unstructured":"Dhanda SK, Vaughan K, Schulten V et al (2018) Development of a novel clustering tool for linear peptide sequences. Immunology 155:331\u2013345. https:\/\/doi.org\/10.1111\/imm.12984","journal-title":"Immunology"},{"key":"6088_CR17","doi-asserted-by":"publisher","first-page":"e1003266","DOI":"10.1371\/journal.pcbi.1003266","volume":"9","author":"JJA Calis","year":"2013","unstructured":"Calis JJA, Maybeno M, Greenbaum JA et al (2013) Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol 9:e1003266. https:\/\/doi.org\/10.1371\/journal.pcbi.1003266","journal-title":"PLoS Comput Biol"},{"key":"6088_CR18","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1186\/1471-2105-8-361","volume":"8","author":"H-H Bui","year":"2007","unstructured":"Bui H-H, Sidney J, Li W et al (2007) Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics 8:361. https:\/\/doi.org\/10.1186\/1471-2105-8-361","journal-title":"BMC Bioinformatics"},{"key":"6088_CR19","doi-asserted-by":"publisher","first-page":"e73957","DOI":"10.1371\/journal.pone.0073957","volume":"8","author":"S Gupta","year":"2013","unstructured":"Gupta S, Kapoor P, Chaudhary K et al (2013) In silico approach for predicting toxicity of peptides and proteins. PLoS ONE 8:e73957. https:\/\/doi.org\/10.1371\/journal.pone.0073957","journal-title":"PLoS ONE"},{"key":"6088_CR20","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1093\/bioinformatics\/btt619","volume":"30","author":"I Dimitrov","year":"2014","unstructured":"Dimitrov I, Naneva L, Doytchinova I, Bangov I (2014) AllergenFP: allergenicity prediction by descriptor fingerprints. Bioinformatics 30:846\u2013851. https:\/\/doi.org\/10.1093\/bioinformatics\/btt619","journal-title":"Bioinformatics"},{"issue":"1","key":"6088_CR21","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 GPS (2013) Designing of interferon-gamma inducing MHC class-II binders. Biol Direct 8(1):1\u201315","journal-title":"Biol Direct"},{"key":"6088_CR22","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/1471-2105-7-153","volume":"7","author":"H-H Bui","year":"2006","unstructured":"Bui H-H, Sidney J, Dinh K et al (2006) Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics 7:153. https:\/\/doi.org\/10.1186\/1471-2105-7-153","journal-title":"BMC Bioinformatics"},{"key":"6088_CR23","doi-asserted-by":"publisher","first-page":"4745","DOI":"10.1021\/ct500592m","volume":"10","author":"Y Shen","year":"2014","unstructured":"Shen Y, Maupetit J, Derreumaux P, Tuff\u00e9ry P (2014) Improved PEP-FOLD approach for peptide and miniprotein structure prediction. J Chem Theory Comput 10:4745\u20134758. https:\/\/doi.org\/10.1021\/ct500592m","journal-title":"J Chem Theory Comput"},{"key":"6088_CR24","doi-asserted-by":"publisher","unstructured":"e Oliveira DMT, de Serpa Brand\u00e3o RMS, da Mata Sousa LCD, et al (2019) pHLA3D: an online database of predicted three-dimensional structures of HLA molecules. Hum Immunol 80:834\u2013841. https:\/\/doi.org\/10.1016\/j.humimm.2019.06.009","DOI":"10.1016\/j.humimm.2019.06.009"},{"key":"6088_CR25","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera\u2014a visualization system for exploratory research and analysis. J Comput Chem 25:1605\u20131612. https:\/\/doi.org\/10.1002\/jcc.20084","journal-title":"J Comput Chem"},{"key":"6088_CR26","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1038\/nprot.2010.5","volume":"5","author":"A Roy","year":"2010","unstructured":"Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5:725\u2013738. https:\/\/doi.org\/10.1038\/nprot.2010.5","journal-title":"Nat Protoc"},{"key":"6088_CR27","doi-asserted-by":"publisher","first-page":"2525","DOI":"10.1016\/j.bpj.2011.10.024","volume":"101","author":"D Xu","year":"2011","unstructured":"Xu D, Zhang Y (2011) Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J 101:2525\u20132534. https:\/\/doi.org\/10.1016\/j.bpj.2011.10.024","journal-title":"Biophys J"},{"key":"6088_CR28","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","volume":"11","author":"JA Maier","year":"2015","unstructured":"Maier JA, Martinez C, Kasavajhala K et al (2015) ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput 11:3696\u20133713. https:\/\/doi.org\/10.1021\/acs.jctc.5b00255","journal-title":"J Chem Theory Comput"},{"key":"6088_CR29","doi-asserted-by":"publisher","first-page":"10096","DOI":"10.1063\/1.1808117","volume":"121","author":"DJ Price","year":"2004","unstructured":"Price DJ, Brooks CL (2004) A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys 121:10096\u201310103. https:\/\/doi.org\/10.1063\/1.1808117","journal-title":"J Chem Phys"},{"key":"6088_CR30","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1002\/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V","volume":"22","author":"V Kr\u00e4utler","year":"2001","unstructured":"Kr\u00e4utler V, van Gunsteren WF, H\u00fcnenberger PH (2001) A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J Comput Chem 22:501\u2013508. https:\/\/doi.org\/10.1002\/1096-987X(20010415)22:5%3c501::AID-JCC1021%3e3.0.CO;2-V","journal-title":"J Comput Chem"},{"key":"6088_CR31","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N \u22c5log( N ) method for Ewald sums in large systems. J Chem Phys 98:10089\u201310092. https:\/\/doi.org\/10.1063\/1.464397","journal-title":"J Chem Phys"},{"key":"6088_CR32","doi-asserted-by":"publisher","first-page":"1587","DOI":"10.1007\/s11030-022-10513-6","volume":"27","author":"R Roy","year":"2023","unstructured":"Roy R, Sk MF, Tanwar O, Kar P (2023) Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease. Mol Divers 27:1587\u20131602. https:\/\/doi.org\/10.1007\/s11030-022-10513-6","journal-title":"Mol Divers"},{"key":"6088_CR33","doi-asserted-by":"publisher","first-page":"1668","DOI":"10.1002\/jcc.20290","volume":"26","author":"DA Case","year":"2005","unstructured":"Case DA, Cheatham TE, Darden T et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668\u20131688. https:\/\/doi.org\/10.1002\/jcc.20290","journal-title":"J Comput Chem"},{"issue":"54","key":"6088_CR34","first-page":"1689","volume":"2013","author":"DA Case","year":"2019","unstructured":"Case DA, Ben-Shalom IY, Brozell SR, Amber, et al (2019) reference manual. J Chem Inf Model 2013(54):1689\u20131699","journal-title":"J Chem Inf Model"},{"key":"6088_CR35","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1107\/S0021889892009944","volume":"26","author":"RA Laskowski","year":"1993","unstructured":"Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283\u2013291. https:\/\/doi.org\/10.1107\/S0021889892009944","journal-title":"J Appl Crystallogr"},{"issue":"11","key":"6088_CR36","doi-asserted-by":"publisher","first-page":"2604","DOI":"10.1093\/emboj\/cdg270","volume":"22","author":"Y Zhang","year":"2003","unstructured":"Zhang Y, Corver J, Chipman PR et al (2003) Structures of immature flavivirus particles. EMBO J 22(11):2604\u20132613","journal-title":"EMBO J"},{"key":"6088_CR37","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1016\/j.molimm.2019.09.014","volume":"114","author":"S Ferdous","year":"2019","unstructured":"Ferdous S, Kelm S, Baker TS et al (2019) B-cell epitopes: discontinuity and conformational analysis. Mol Immunol 114:643\u2013650. https:\/\/doi.org\/10.1016\/j.molimm.2019.09.014","journal-title":"Mol Immunol"},{"key":"6088_CR38","doi-asserted-by":"publisher","first-page":"W24","DOI":"10.1093\/nar\/gkx346","volume":"45","author":"MC Jespersen","year":"2017","unstructured":"Jespersen MC, Peters B, Nielsen M, Marcatili P (2017) BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res 45:W24\u2013W29. https:\/\/doi.org\/10.1093\/nar\/gkx346","journal-title":"Nucleic Acids Res"},{"key":"6088_CR39","doi-asserted-by":"publisher","first-page":"D339","DOI":"10.1093\/nar\/gky1006","volume":"47","author":"R Vita","year":"2019","unstructured":"Vita R, Mahajan S, Overton JA et al (2019) The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res 47:D339\u2013D343. https:\/\/doi.org\/10.1093\/nar\/gky1006","journal-title":"Nucleic Acids Res"},{"key":"6088_CR40","doi-asserted-by":"publisher","first-page":"338","DOI":"10.3390\/v9110338","volume":"9","author":"X Zhang","year":"2017","unstructured":"Zhang X, Jia R, Shen H et al (2017) Structures and functions of the envelope glycoprotein in Flavivirus infections. Viruses 9:338. https:\/\/doi.org\/10.3390\/v9110338","journal-title":"Viruses"},{"key":"6088_CR41","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1038\/s41467-018-02882-0","volume":"9","author":"T F\u00fczik","year":"2018","unstructured":"F\u00fczik T, Formanov\u00e1 P, R\u016f\u017eek D et al (2018) Structure of tick-borne encephalitis virus and its neutralization by a monoclonal antibody. Nat Commun 9:436. https:\/\/doi.org\/10.1038\/s41467-018-02882-0","journal-title":"Nat Commun"},{"key":"6088_CR42","doi-asserted-by":"publisher","first-page":"e82447","DOI":"10.7554\/eLife.82447","volume":"12","author":"L Zuzic","year":"2023","unstructured":"Zuzic L, Marzinek JK, Anand GS et al (2023) A pH-dependent cluster of charges in a conserved cryptic pocket on flaviviral envelopes. Elife 12:e82447. https:\/\/doi.org\/10.7554\/eLife.82447","journal-title":"Elife"},{"key":"6088_CR43","unstructured":"DeLano WL (2002) The PyMOL molecular graphics system, version 1. Schr\u00f6dinger, LLC"},{"key":"6088_CR44","doi-asserted-by":"publisher","first-page":"e1002829","DOI":"10.1371\/journal.pcbi.1002829","volume":"8","author":"JV Kringelum","year":"2012","unstructured":"Kringelum JV, Lundegaard C, Lund O, Nielsen M (2012) Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Comput Biol 8:e1002829. https:\/\/doi.org\/10.1371\/journal.pcbi.1002829","journal-title":"PLoS Comput Biol"},{"key":"6088_CR45","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1016\/j.chom.2016.04.013","volume":"19","author":"L Dai","year":"2016","unstructured":"Dai L, Song J, Lu X et al (2016) Structures of the Zika virus envelope protein and its complex with a Flavivirus broadly protective antibody. Cell Host Microbe 19:696\u2013704. https:\/\/doi.org\/10.1016\/j.chom.2016.04.013","journal-title":"Cell Host Microbe"},{"key":"6088_CR46","doi-asserted-by":"publisher","first-page":"e16059","DOI":"10.1371\/journal.pone.0016059","volume":"6","author":"Y-Q Deng","year":"2011","unstructured":"Deng Y-Q, Dai J-X, Ji G-H et al (2011) A broadly Flavivirus cross-neutralizing monoclonal antibody that recognizes a novel epitope within the fusion loop of E protein. PLoS ONE 6:e16059. https:\/\/doi.org\/10.1371\/journal.pone.0016059","journal-title":"PLoS ONE"},{"key":"6088_CR47","doi-asserted-by":"publisher","first-page":"3269","DOI":"10.1038\/emboj.2009.245","volume":"28","author":"MV Cherrier","year":"2009","unstructured":"Cherrier MV, Kaufmann B, Nybakken GE et al (2009) Structural basis for the preferential recognition of immature flaviviruses by a fusion-loop antibody. EMBO J 28:3269\u20133276. https:\/\/doi.org\/10.1038\/emboj.2009.245","journal-title":"EMBO J"},{"key":"6088_CR48","doi-asserted-by":"publisher","first-page":"e1000060","DOI":"10.1371\/journal.ppat.1000060","volume":"4","author":"S Nelson","year":"2008","unstructured":"Nelson S, Jost CA, Xu Q et al (2008) Maturation of West Nile virus modulates sensitivity to antibody-mediated neutralization. PLoS Pathog 4:e1000060. https:\/\/doi.org\/10.1371\/journal.ppat.1000060","journal-title":"PLoS Pathog"},{"key":"6088_CR49","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1038\/nature18938","volume":"536","author":"G Barba-Spaeth","year":"2016","unstructured":"Barba-Spaeth G, Dejnirattisai W, Rouvinski A et al (2016) Structural basis of potent Zika\u2013dengue virus antibody cross-neutralization. Nature 536:48\u201353. https:\/\/doi.org\/10.1038\/nature18938","journal-title":"Nature"},{"key":"6088_CR50","doi-asserted-by":"publisher","first-page":"W636","DOI":"10.1093\/nar\/gkz268","volume":"47","author":"F Madeira","year":"2019","unstructured":"Madeira F, Park YM, Lee J et al (2019) The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res 47:W636\u2013W641. https:\/\/doi.org\/10.1093\/nar\/gkz268","journal-title":"Nucleic Acids Res"},{"key":"6088_CR51","doi-asserted-by":"publisher","first-page":"W320","DOI":"10.1093\/nar\/gku316","volume":"42","author":"X Robert","year":"2014","unstructured":"Robert X, Gouet P (2014) Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 42:W320\u2013W324. https:\/\/doi.org\/10.1093\/nar\/gku316","journal-title":"Nucleic Acids Res"},{"key":"6088_CR52","doi-asserted-by":"publisher","first-page":"1016","DOI":"10.1016\/j.cell.2016.07.020","volume":"166","author":"H Zhao","year":"2016","unstructured":"Zhao H, Fernandez E, Dowd KA et al (2016) Structural basis of Zika virus-specific antibody protection. Cell 166:1016\u20131027. https:\/\/doi.org\/10.1016\/j.cell.2016.07.020","journal-title":"Cell"},{"key":"6088_CR53","doi-asserted-by":"publisher","first-page":"e1002930","DOI":"10.1371\/journal.ppat.1002930","volume":"8","author":"SK Austin","year":"2012","unstructured":"Austin SK, Dowd KA, Shrestha B et al (2012) Structural basis of differential neutralization of DENV-1 genotypes by an antibody that recognizes a cryptic epitope. PLoS Pathog 8:e1002930. https:\/\/doi.org\/10.1371\/journal.ppat.1002930","journal-title":"PLoS Pathog"},{"key":"6088_CR54","doi-asserted-by":"publisher","first-page":"e1004072","DOI":"10.1371\/journal.ppat.1004072","volume":"10","author":"MA Edeling","year":"2014","unstructured":"Edeling MA, Austin SK, Shrestha B et al (2014) Potent dengue virus neutralization by a therapeutic antibody with low monovalent affinity requires bivalent engagement. PLoS Pathog 10:e1004072. https:\/\/doi.org\/10.1371\/journal.ppat.1004072","journal-title":"PLoS Pathog"},{"issue":"8","key":"6088_CR55","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/JVI.02132-18","volume":"93","author":"X Yang","year":"2019","unstructured":"Yang X, Qi J, Peng R et al (2019) Molecular basis of a protective\/neutralizing monoclonal antibody targeting envelope proteins of both tick-borne encephalitis virus and Louping ill virus. J Virol 93(8):10\u2013128. https:\/\/doi.org\/10.1128\/JVI.02132-18","journal-title":"J Virol"},{"key":"6088_CR56","doi-asserted-by":"publisher","first-page":"1248","DOI":"10.1038\/s41590-018-0227-7","volume":"19","author":"M Renner","year":"2018","unstructured":"Renner M, Flanagan A, Dejnirattisai W et al (2018) Characterization of a potent and highly unusual minimally enhancing antibody directed against dengue virus. Nat Immunol 19:1248\u20131256. https:\/\/doi.org\/10.1038\/s41590-018-0227-7","journal-title":"Nat Immunol"},{"key":"6088_CR57","doi-asserted-by":"publisher","first-page":"1385","DOI":"10.1016\/j.celrep.2018.10.031","volume":"25","author":"JR Keeffe","year":"2018","unstructured":"Keeffe JR, Van Rompay KKA, Olsen PC et al (2018) A combination of two human monoclonal antibodies prevents Zika virus escape mutations in non-human primates. Cell Rep 25:1385-1394.e7. https:\/\/doi.org\/10.1016\/j.celrep.2018.10.031","journal-title":"Cell Rep"},{"issue":"369","key":"6088_CR58","doi-asserted-by":"publisher","first-page":"369ra179","DOI":"10.1126\/scitranslmed.aai8336","volume":"8","author":"Q Wang","year":"2016","unstructured":"Wang Q, Yang H, Liu X et al (2016) Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus. Sci Transl Med 8(369):369ra179. https:\/\/doi.org\/10.1126\/scitranslmed.aai8336","journal-title":"Sci Transl Med"}],"container-title":["Journal of Molecular Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-024-06088-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00894-024-06088-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-024-06088-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,13]],"date-time":"2024-08-13T21:18:11Z","timestamp":1723583891000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00894-024-06088-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,31]]},"references-count":58,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2024,8]]}},"alternative-id":["6088"],"URL":"https:\/\/doi.org\/10.1007\/s00894-024-06088-8","relation":{},"ISSN":["1610-2940","0948-5023"],"issn-type":[{"type":"print","value":"1610-2940"},{"type":"electronic","value":"0948-5023"}],"subject":[],"published":{"date-parts":[[2024,7,31]]},"assertion":[{"value":"17 December 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 July 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 July 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"295"}}