{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T19:08:36Z","timestamp":1783796916409,"version":"3.55.0"},"reference-count":127,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T00:00:00Z","timestamp":1772668800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Med."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Prostate cancer remains a major global health challenge, necessitating precision immunotherapeutic strategies tailored to tumor-associated antigens. This study aimed to design a multi-epitope peptide vaccine targeting prostate-specific membrane antigen (PSMA), six-transmembrane epithelial antigen of prostate 1 (STEAP1), and B7-H3, three biomarkers strongly associated with prostate cancer progression.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>A multi-layered immunoinformatics-driven approach was employed, integrating epitope prediction, antigenicity and immunogenicity assessment, allergenicity and toxicity screening, population coverage analysis, molecular docking, and molecular dynamics simulations. Selected epitopes were assembled into a vaccine construct using appropriate adjuvants and linkers to enhance immune activation and structural stability.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The designed vaccine construct demonstrated extensive global HLA allele coverage (97.51%), strong binding affinity to B-cell receptors, MHC molecules, and favorable structural stability during molecular dynamics simulations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>These findings suggest that the proposed multi-epitope vaccine represents a promising immunotherapeutic candidate for prostate cancer and warrants further experimental validation.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmed.2026.1716345","type":"journal-article","created":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T05:25:36Z","timestamp":1772688336000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Immunoinformatics-driven multi-epitope vaccine design targeting PSMA, STEAP1, and B7H3 for prostate cancer"],"prefix":"10.3389","volume":"13","author":[{"given":"Stefanus Vicky Bernhard Elisa","family":"Runtunuwu","sequence":"first","affiliation":[{"name":"Medical Education Study Program, Faculty of Medicine, Sam Ratulangi University","place":["Manado, Indonesia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trina Ekawati","family":"Tallei","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Medicine, Sam Ratulangi University","place":["Manado, Indonesia"]},{"name":"Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University","place":["Manado, Indonesia"]},{"name":"Department of Pathology, College of Korean Medicine, Kyung Hee University","place":["Seoul, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyo Jeong","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Pathology, College of Korean Medicine, Kyung Hee University","place":["Seoul, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moon Nyeo","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Pathology, College of Korean Medicine, Kyung Hee University","place":["Seoul, Republic of Korea"]},{"name":"Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University","place":["Seoul, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ismail","family":"Celik","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University","place":["Kayseri, T\u00fcrkiye"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Burak","family":"Kirilmaz","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University","place":["Kayseri, T\u00fcrkiye"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grace Lendawati Amelia","family":"Turalaki","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Medicine, Sam Ratulangi University","place":["Manado, Indonesia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatimawali","family":"Fatimawali","sequence":"additional","affiliation":[{"name":"Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University","place":["Manado, Indonesia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lydia Estelina Naomi","family":"Tendean","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Medicine, Sam Ratulangi University","place":["Manado, Indonesia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martha Marie","family":"Kaseke","sequence":"additional","affiliation":[{"name":"Department of Anatomy and Histology, Faculty of Medicine, Sam Ratulangi University","place":["Manado, Indonesia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dionisius Rafael","family":"Makawaehe","sequence":"additional","affiliation":[{"name":"Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University","place":["Manado, Indonesia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elne Vieke","family":"Rambi","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratory Technology, Politeknik Kesehatan Kemenkes Manado","place":["Manado, Indonesia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bonglee","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Pathology, College of Korean Medicine, Kyung Hee University","place":["Seoul, Republic of Korea"]},{"name":"Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University","place":["Seoul, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,3,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/j.eururo.2024.11.013","article-title":"Recent patterns and trends in global prostate cancer incidence and mortality: an update","volume":"87","author":"Schafer","year":"2024","journal-title":"Eur Urol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"485","DOI":"10.3322\/caac.70028","article-title":"Prostate cancer statistics, 2025","volume":"75","author":"Kratzer","year":"2025","journal-title":"CA Cancer J Clin."},{"key":"B3","doi-asserted-by":"publisher","first-page":"5730","DOI":"10.3390\/molecules27175730","article-title":"Prostate cancer review: genetics, diagnosis, treatment options, and alternative approaches","volume":"27","author":"Sekhoacha","year":"2022","journal-title":"Molecules."},{"key":"B4","doi-asserted-by":"publisher","first-page":"561","DOI":"10.2217\/14796694.4.4.561","article-title":"Prostate cancer: psychosocial implications and management","volume":"4","author":"Roth","year":"2008","journal-title":"Future Oncol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"44","DOI":"10.17925\/EOH.2020.16.1.44","article-title":"Immunotherapy in advanced prostate cancer","volume":"16","author":"Randhawa","year":"2020","journal-title":"Eur Oncol Haematol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"3867","DOI":"10.1158\/1078-0432.CCR-11-0943","article-title":"Translating scientific advancement into clinical benefit for castration-resistant prostate cancer patients","volume":"17","author":"Attard","year":"2011","journal-title":"Clin Cancer Res."},{"key":"B7","doi-asserted-by":"publisher","first-page":"3335","DOI":"10.1172\/JCI83871","article-title":"Cancer immunotherapy: harnessing the immune system to battle cancer","volume":"125","author":"Yang","year":"2015","journal-title":"J Clin Invest."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1783","DOI":"10.3390\/vaccines11121783","article-title":"Cancer vaccines in the immunotherapy era: promise and potential","volume":"11","author":"Verma","year":"2023","journal-title":"Vaccines."},{"key":"B9","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1038\/s41392-023-01674-3","article-title":"Therapeutic cancer vaccines: advancements, challenges and prospects","volume":"8","author":"Fan","year":"2023","journal-title":"Signal Transduct Target Ther."},{"key":"B10","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1056\/NEJMoa1001294","article-title":"Sipuleucel-T immunotherapy for castration-resistant prostate cancer","volume":"363","author":"Kantoff","year":"2010","journal-title":"N Engl J Med."},{"key":"B11","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1038\/s41585-023-00739-w","article-title":"Vaccines as treatments for prostate cancer","volume":"20","author":"Rastogi","year":"2023","journal-title":"Nat Rev Urol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1016\/j.eururo.2018.08.009","article-title":"Multifocal primary prostate cancer exhibits high degree of genomic heterogeneity","volume":"3","author":"L\u00f8vf","year":"2019","journal-title":"Eur Urol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1186\/PREACCEPT-1882913817126479","article-title":"Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer","volume":"15","author":"Wyatt","year":"2014","journal-title":"Genome Biol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"2159","DOI":"10.3390\/cells12172159","article-title":"Cancer vaccine therapeutics: limitations and effectiveness\u2014a literature review","volume":"12","author":"Kaczmarek","year":"2023","journal-title":"Cells."},{"key":"B15","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1186\/s12964-024-01776-7","article-title":"The complex interplay of tumor-infiltrating cells in driving therapeutic resistance pathways","volume":"22","author":"Li","year":"2024","journal-title":"Cell Commun Signal."},{"key":"B16","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1038\/cmi.2017.92","article-title":"Multi-epitope vaccines: a promising strategy against tumors and viral infections","volume":"15","author":"Zhang","year":"2017","journal-title":"Cell Mol Immunol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1007\/s13596-023-00697-z","article-title":"In silico approaches for study the therapeutic potential of Cannabis sativa (Bhang) against HIV","volume":"24","author":"Kajal","year":"2023","journal-title":"Adv Tradit Med."},{"key":"B18","doi-asserted-by":"publisher","first-page":"931612","DOI":"10.3389\/fimmu.2022.931612","article-title":"Potential association factors for developing effective peptide-based cancer vaccines","volume":"13","author":"Jiang","year":"2022","journal-title":"Front Immunol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1016\/j.trecan.2024.05.003","article-title":"B7-H3: a robust target for immunotherapy in prostate cancer","volume":"10","author":"Pulido","year":"2024","journal-title":"Trends Cancer."},{"key":"B20","doi-asserted-by":"crossref","first-page":"139","DOI":"10.36255\/exonpublications.prostatecancer.steap.2021","article-title":"The usefulness of STEAP proteins in prostate cancer clinical practice","volume-title":"Prostate Cancer","author":"Rocha","year":"2021"},{"key":"B21","doi-asserted-by":"publisher","first-page":"14523","DOI":"10.1073\/pnas.96.25.14523","article-title":"STEAP: a prostate-specific cell-surface antigen highly expressed in human prostate tumors","volume":"25","author":"Hubert","year":"1999","journal-title":"Proc Natl Acad Sci USA."},{"key":"B22","doi-asserted-by":"publisher","first-page":"12590","DOI":"10.1073\/pnas.1735443100","article-title":"The homodimer of prostate-specific membrane antigen is a functional target for cancer therapy","volume":"100","author":"Sch\u00fclke","year":"2003","journal-title":"Proc Natl Acad Sci USA."},{"key":"B23","doi-asserted-by":"publisher","first-page":"119","DOI":"10.20517\/jtgg.2023.50","article-title":"New approaches and prospects of immunotherapy and gene therapy for prostate cancer","volume":"8","author":"Bibi","year":"2024","journal-title":"J Transl Genet Genom."},{"key":"B24","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1038\/s41698-024-00599-6","article-title":"Assessment of TROP2, CEACAM5 and DLL3 in metastatic prostate cancer: expression landscape and molecular correlates","volume":"8","author":"Ajkunic","year":"2024","journal-title":"NPJ Precis Oncol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"2029","DOI":"10.1021\/acs.molpharmaceut.4c01252","article-title":"E-urea-K-based PSMA imaging served as an alternative in assessing tumor neovascularization via targeting CD31","volume":"22","author":"Wang","year":"2025","journal-title":"Mol Pharm."},{"key":"B26","doi-asserted-by":"publisher","first-page":"794","DOI":"10.3390\/biomedicines13040794","article-title":"The role of STEAP1 in prostate cancer: implications for diagnosis and therapeutic strategies","volume":"13","author":"Zhang","year":"2025","journal-title":"Biomedicines."},{"key":"B27","doi-asserted-by":"publisher","first-page":"114890","DOI":"10.1016\/j.biopha.2023.114890","article-title":"B7-H3 immunoregulatory roles in cancer","volume":"163","author":"Mortezaee","year":"2023","journal-title":"Biomed Pharmacother."},{"key":"B28","doi-asserted-by":"publisher","first-page":"D10","DOI":"10.1093\/nar\/gkaa892","article-title":"Database resources of the national center for biotechnology information","volume":"49","author":"Sayers","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B29","doi-asserted-by":"publisher","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"B30","doi-asserted-by":"publisher","first-page":"W24","DOI":"10.1093\/nar\/gkx346","article-title":"Marcatili P. BepiPred-20: improving sequence-based B-cell epitope prediction using conformational epitopes","volume":"45","author":"Jespersen","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"B31","doi-asserted-by":"publisher","first-page":"856","DOI":"10.1016\/j.vaccine.2006.09.032","article-title":"Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties","volume":"25","author":"Doytchinova","year":"2007","journal-title":"Vaccine."},{"key":"B32","doi-asserted-by":"publisher","first-page":"3360","DOI":"10.4049\/jimmunol.1700893","article-title":"Nielsen M. NetMHCpan-4.0: improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data","volume":"199","author":"Jurtz","year":"2017","journal-title":"J Immunol"},{"key":"B33","doi-asserted-by":"publisher","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","article-title":"NetMHCpan-4","volume":"48","author":"Reynisson","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"B34","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1002\/cpim.12","article-title":"TepiTool: a pipeline for computational prediction of T cell epitope candidates","volume":"114","author":"Paul","year":"2016","journal-title":"Curr Protoc Immunol"},{"key":"B35","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/nri3084","article-title":"Towards a systems understanding of MHC class I and MHC class II antigen presentation","volume":"11","author":"Neefjes","year":"2011","journal-title":"Nat Rev Immunol."},{"key":"B36","doi-asserted-by":"publisher","first-page":"E2046","DOI":"10.1073\/pnas.1305227110","article-title":"Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells","volume":"110","author":"Weiskopf","year":"2013","journal-title":"Proc Natl Acad Sci USA."},{"key":"B37","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1007\/s00251-011-0513-0","article-title":"Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes","volume":"63","author":"Greenbaum","year":"2011","journal-title":"Immunogenetics."},{"key":"B38","doi-asserted-by":"publisher","first-page":"W408","DOI":"10.1093\/nar\/gkv451","article-title":"CCTOP: a consensus constrained topology prediction web server","volume":"43","author":"Dobson","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B39","doi-asserted-by":"publisher","first-page":"24046","DOI":"10.1038\/s41598-025-03672-7","article-title":"Design of a novel multiepitope vaccine against glioblastoma by in silico approaches","volume":"15","author":"Mirzaie","year":"2025","journal-title":"Sci Rep."},{"key":"B40","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1016\/j.immuni.2010.09.017","article-title":"Reverse vaccinology: developing vaccines in the era of genomics","volume":"33","author":"Sette","year":"2010","journal-title":"Immunity."},{"key":"B41","doi-asserted-by":"publisher","first-page":"e4785","DOI":"10.1002\/pro.4785","article-title":"Multi-perspectives and challenges in identifying B-cell epitopes","volume":"32","author":"Kumar","year":"2023","journal-title":"Protein Sci."},{"key":"B42","doi-asserted-by":"publisher","first-page":"102180","DOI":"10.1016\/j.trim.2025.102180","article-title":"Study of human leukocyte antigen (HLA) allele and haplotype frequency using next generation sequencing (NGS) platform: single-centre study of over 500 individuals in India! Transpl Immunol","volume":"89","author":"Simmi","year":"2025"},{"key":"B43","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/1471-2105-7-153","article-title":"Predicting population coverage of T-cell epitope-based diagnostics and vaccines","volume":"7","author":"Bui","year":"2006","journal-title":"BMC Bioinformatics."},{"key":"B44","doi-asserted-by":"publisher","first-page":"e115711","DOI":"10.1371\/journal.pone.0115711","article-title":"Cancer immunotherapy employing an innovative strategy to enhance CD4+ T cell help in the tumor microenvironment","volume":"9","author":"Song","year":"2014","journal-title":"PLoS ONE."},{"key":"B45","doi-asserted-by":"publisher","first-page":"1357","DOI":"10.1016\/j.addr.2012.09.039","article-title":"Fusion protein linkers: property, design and functionality","volume":"65","author":"Chen","year":"2013","journal-title":"Adv Drug Deliv Rev."},{"key":"B46","doi-asserted-by":"publisher","first-page":"5499","DOI":"10.4049\/jimmunol.168.11.5499","article-title":"A rational strategy to design multiepitope immunogens based on multiple Th lymphocyte epitopes","volume":"168","author":"Livingston","year":"2002","journal-title":"J Immunol"},{"key":"B47","doi-asserted-by":"publisher","first-page":"24485","DOI":"10.1038\/s41598-021-03932-2","article-title":"Designing a multi-epitope vaccine to provoke the robust immune response against influenza A H7N9","volume":"11","author":"Tarrahimofrad","year":"2021","journal-title":"Sci Rep."},{"key":"B48","doi-asserted-by":"publisher","first-page":"1104","DOI":"10.1016\/j.tips.2024.10.013","article-title":"Challenges and considerations in multi-epitope vaccine design surrounding toll-like receptors","volume":"45","author":"Shah","year":"2024","journal-title":"Trends Pharmacol Sci."},{"key":"B49","doi-asserted-by":"publisher","first-page":"2278","DOI":"10.1007\/s00894-014-2278-5","article-title":"AllerTOP v2\u2014a server for in silico prediction of allergens","volume":"20","author":"Dimitrov","year":"2014","journal-title":"J Mol Model"},{"key":"B50","doi-asserted-by":"publisher","first-page":"W202","DOI":"10.1093\/nar\/gkl343","article-title":"AlgPred: prediction of allergenic proteins and mapping of IgE epitopes","volume":"34","author":"Saha","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"B51","doi-asserted-by":"publisher","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":"Comput Appl Biosci."},{"key":"B52","doi-asserted-by":"publisher","first-page":"W287","DOI":"10.1093\/nar\/gkae328","article-title":"Deep learning for the PSIPRED protein analysis workbench","volume":"52","author":"Buchan","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B53","doi-asserted-by":"publisher","first-page":"W349","DOI":"10.1093\/nar\/gkt381","article-title":"Scalable web services for the PSIPRED protein analysis workbench","volume":"41","author":"Buchan","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"B54","doi-asserted-by":"publisher","first-page":"W402","DOI":"10.1093\/nar\/gkz297","article-title":"The PSIPRED protein analysis workbench: 20 years on","volume":"47","author":"Buchan","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B55","doi-asserted-by":"publisher","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":"B56","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1038\/nmeth.3213","article-title":"The I-TASSER suite: protein structure and function prediction","volume":"12","author":"Yang","year":"2014","journal-title":"Nat Methods."},{"key":"B57","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1002\/prot.22588","article-title":"I-TASSER: fully automated protein structure prediction in CASP8","volume":"77","author":"Zhang","year":"2009","journal-title":"Proteins."},{"key":"B58","doi-asserted-by":"publisher","first-page":"2195","DOI":"10.1002\/pro.3274","article-title":"Homology modeling in a dynamical world","volume":"26","author":"Monzon","year":"2017","journal-title":"Protein Sci."},{"key":"B59","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: a program to check the stereochemical quality of protein structures","volume":"26","author":"Laskowski","year":"1993","journal-title":"J Appl Crystallogr."},{"key":"B60","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1038\/nprot.2016.169","article-title":"The ClusPro web server for protein\u2013protein docking","volume":"12","author":"Kozakov","year":"2017","journal-title":"Nat Protoc."},{"key":"B61","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1002\/prot.25219","article-title":"New additions to the ClusPro server motivated by CAPRI","volume":"85","author":"Vajda","year":"2017","journal-title":"Proteins."},{"key":"B62","doi-asserted-by":"publisher","first-page":"2159","DOI":"10.1002\/prot.24403","article-title":"How good is automated protein docking?","volume":"81","author":"Kozakov","year":"2013","journal-title":"Proteins."},{"key":"B63","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1107\/S2059798322002741","article-title":"Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap","volume":"78","author":"Jones","year":"2022","journal-title":"Acta Crystallogr D Struct Biol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"1071","DOI":"10.1016\/j.str.2020.06.006","article-title":"Performance and its limits in rigid body protein-protein docking","volume":"28","author":"Desta","year":"2020","journal-title":"Structure"},{"key":"B65","doi-asserted-by":"publisher","first-page":"3676","DOI":"10.1093\/bioinformatics\/btw514","article-title":"PRODIGY: a web server for predicting the binding affinity of protein-protein complexes","volume":"32","author":"Xue","year":"2016","journal-title":"Bioinformatics."},{"key":"B66","volume-title":"The PyMOL Molecular Graphics System","author":"DeLano","year":"2002"},{"key":"B67","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"2","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"B68","doi-asserted-by":"publisher","first-page":"1209","DOI":"10.1016\/j.dib.2016.07.043","article-title":"Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field","volume":"8","author":"Yang","year":"2016","journal-title":"Data Brief."},{"key":"B69","doi-asserted-by":"publisher","first-page":"234505","DOI":"10.1063\/1.2121687","article-title":"A general purpose model for the condensed phases of water: TIP4P\/2005","volume":"123","author":"Abascal","year":"2005","journal-title":"J Chem Phys"},{"key":"B70","doi-asserted-by":"publisher","first-page":"4288","DOI":"10.1039\/D1RA06532G","article-title":"Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods","volume":"12","author":"Rafi","year":"2022","journal-title":"RSC Adv"},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1101\/2021.01.07.425621","article-title":"Molecular dynamics simulations and functional studies reveal that hBD-2 binds SARS-CoV-2 spike RBD and blocks viral entry into ACE2 expressing cells","author":"Zhang","year":"2021","journal-title":"bioRxiv."},{"key":"B72","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.1007\/s11030-022-10539-w","article-title":"Designing a novel SOX9 based multi-epitope vaccine to combat metastatic triple-negative breast cancer using immunoinformatics approach","volume":"27","author":"Krishnamoorthy","year":"2022","journal-title":"Mol Divers."},{"key":"B73","doi-asserted-by":"publisher","first-page":"906","DOI":"10.1016\/j.xphs.2023.11.025","article-title":"Immunoinformatics-driven strategies for advancing epitope-based vaccine design for West Nile virus","volume":"113","author":"Windah","year":"2023","journal-title":"J Pharm Sci."},{"key":"B74","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/life8010001","article-title":"Hydrogen bonds and life in the universe","volume":"8","author":"Vladilo","year":"2018","journal-title":"Life"},{"key":"B75","doi-asserted-by":"publisher","first-page":"1771","DOI":"10.3390\/ijms23031771","article-title":"Molecular docking and molecular dynamics simulations discover curcumin analogue as a plausible dual inhibitor for SARS-CoV-2","volume":"23","author":"Rampogu","year":"2022","journal-title":"Int J Mol Sci."},{"key":"B76","doi-asserted-by":"publisher","first-page":"34984","DOI":"10.1038\/srep34984","article-title":"Structural insights into conformational stability of both wild-type and mutant EZH2 receptor","volume":"6","author":"Aier","year":"2016","journal-title":"Sci Rep."},{"key":"B77","doi-asserted-by":"publisher","first-page":"e9862","DOI":"10.1371\/journal.pone.0009862","article-title":"Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system","volume":"5","author":"Rapin","year":"2010","journal-title":"PLoS ONE."},{"key":"B78","first-page":"197","article-title":"Sipuleucel-T (provenge) injection: the first immunotherapy agent (vaccine) for hormone-refractory prostate cancer","volume":"36","author":"Anassi","year":"2011","journal-title":"P T."},{"key":"B79","doi-asserted-by":"publisher","first-page":"646972","DOI":"10.3389\/fimmu.2021.646972","article-title":"From infection to immunity: understanding the response to SARS-CoV2 through in-silico modeling","volume":"12","author":"Castiglione","year":"2020","journal-title":"Front Immunol"},{"key":"B80","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1086\/589862","article-title":"Vaccines: correlates of vaccine-induced immunity","volume":"3","author":"Plotkin","year":"2008","journal-title":"Clin Infect Dis."},{"key":"B81","doi-asserted-by":"publisher","first-page":"1078","DOI":"10.1016\/j.copbio.2013.02.015","article-title":"Vaccine design: emerging concepts and renewed optimism","volume":"6","author":"Grimm","year":"2013","journal-title":"Curr Opin Biotechnol."},{"key":"B82","doi-asserted-by":"publisher","first-page":"264","DOI":"10.3389\/fonc.2018.00264","article-title":"B7H3 as a promoter of metastasis and promising therapeutic target","volume":"8","author":"Dong","year":"2018","journal-title":"Front Oncol."},{"key":"B83","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1038\/s41420-023-01453-7","article-title":"B7-H3 specific CAR-T cells exhibit potent activity against prostate cancer","volume":"9","author":"Li","year":"2023","journal-title":"Cell Death Discov."},{"key":"B84","doi-asserted-by":"publisher","first-page":"188783","DOI":"10.1016\/j.bbcan.2022.188783","article-title":"To kill a cancer: targeting the immune inhibitory checkpoint molecule, B7-H3","volume":"1877","author":"Kanchan","year":"2022","journal-title":"Biochim Biophys Acta Rev Cancer."},{"key":"B85","doi-asserted-by":"publisher","first-page":"19458","DOI":"10.1073\/pnas.0709802104","article-title":"B7-H3 and B7x are highly expressed in human prostate cancer and associated with disease spread and poor outcome","volume":"104","author":"Zang","year":"2007","journal-title":"Proc Natl Acad Sci USA."},{"key":"B86","doi-asserted-by":"publisher","first-page":"16022","DOI":"10.3390\/ijms242216022","article-title":"Prostate-specific membrane antigen (PSMA) expression predicts need for early treatment in prostate cancer patients managed with active surveillance","volume":"24","author":"Ahmadi","year":"2023","journal-title":"Int J Mol Sci."},{"key":"B87","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.bbrc.2012.10.123","article-title":"STEAP1 is overexpressed in cancers: a promising therapeutic target","volume":"429","author":"Moreaux","year":"2012","journal-title":"Biochem Biophys Res Commun."},{"key":"B88","doi-asserted-by":"publisher","first-page":"1285661","DOI":"10.3389\/fonc.2023.1285661","article-title":"Targeting STEAP1 as an anticancer strategy","volume":"13","author":"Nakamura","year":"2023","journal-title":"Front Oncol."},{"key":"B89","doi-asserted-by":"publisher","first-page":"1388","DOI":"10.1182\/blood-2006-02-003681","article-title":"The Steap proteins are metalloreductases","volume":"108","author":"Ohgami","year":"2006","journal-title":"Blood."},{"key":"B90","doi-asserted-by":"publisher","first-page":"e78","DOI":"10.1002\/qub2.78","article-title":"Bioinformatics perspectives on transcriptomics: a comprehensive review of bulk and single-cell RNA sequencing analyses","volume":"13","author":"Tzec-Interi\u00e1n","year":"2025","journal-title":"Quant Biol."},{"key":"B91","doi-asserted-by":"publisher","first-page":"836","DOI":"10.3390\/vaccines12080836","article-title":"Tumor neoepitope-based vaccines: a scoping review on current predictive computational strategies","volume":"12","author":"Rocha","year":"2024","journal-title":"Vaccines."},{"key":"B92","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3892\/ijo.2025.5749","article-title":"Strategies for neoantigen screening and immunogenicity validation in cancer immunotherapy (review)","volume":"66","author":"Feng","year":"2025","journal-title":"Int J Oncol."},{"key":"B93","doi-asserted-by":"publisher","first-page":"120139","DOI":"10.1098\/rsob.120139","article-title":"T-cell epitope vaccine design by immunoinformatics","volume":"3","author":"Patronov","year":"2013","journal-title":"Open Biol"},{"key":"B94","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1039\/C5SC03892H","article-title":"Peptide-based synthetic vaccines","volume":"7","author":"Skwarczynski","year":"2015","journal-title":"Chem Sci."},{"key":"B95","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/s13045-022-01247-x","article-title":"Cancer vaccines as promising immuno-therapeutics: platforms and current progress","volume":"15","author":"Liu","year":"2022","journal-title":"J Hematol Oncol."},{"key":"B96","doi-asserted-by":"publisher","first-page":"1007285","DOI":"10.3389\/fimmu.2022.1007285","article-title":"The long multi-epitope peptide vaccine combined with adjuvants improved the therapeutic effects in a glioblastoma mouse model","volume":"13","author":"Tran","year":"2022","journal-title":"Front Immunol."},{"key":"B97","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/j.imlet.2004.01.006","article-title":"The pan HLA DR-binding epitope improves adjuvant-assisted immunization with a recombinant protein containing a malaria vaccine candidate","volume":"3","author":"Rosa","year":"2004","journal-title":"Immunol Lett."},{"key":"B98","doi-asserted-by":"publisher","first-page":"621706","DOI":"10.3389\/fimmu.2021.621706","article-title":"Immunoinformatics design of multi-epitope peptide-based vaccine against schistosoma mansoni using transmembrane proteins as a target","volume":"12","author":"Sanches","year":"2021","journal-title":"Front Immunol."},{"key":"B99","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.3389\/fimmu.2020.01165","article-title":"Peptide vaccine combined adjuvants modulate anti-tumor effects of radiation in glioblastoma mouse model","volume":"11","author":"Tran","year":"2020","journal-title":"Front Immunol."},{"key":"B100","doi-asserted-by":"publisher","first-page":"3401","DOI":"10.1172\/JCI80009","article-title":"Therapeutic cancer vaccines","volume":"125","author":"Melief","year":"2015","journal-title":"J Clin Invest."},{"key":"B101","doi-asserted-by":"publisher","first-page":"201000","DOI":"10.1016\/j.omton.2025.201000","article-title":"Novel synthetic peptide-based vaccine shows promise against prostate cancer","volume":"33","author":"V\u00e1zquez-Arregu\u00edn","year":"2025","journal-title":"Mol Ther Oncol."},{"key":"B102","doi-asserted-by":"publisher","first-page":"797","DOI":"10.3390\/biology11050797","article-title":"An insight based on computational analysis of the interaction between the receptor-binding domain of the Omicron variants and human angiotensin-converting enzyme 2","volume":"11","author":"Celik","year":"2022","journal-title":"Biology."},{"key":"B103","doi-asserted-by":"publisher","first-page":"6307457","DOI":"10.20944\/preprints202004.0102.v1","article-title":"Potential of plant bioactive compounds as SARS-CoV-2 main protease (Mpro) and spike (S) glycoprotein inhibitors: a molecular docking study","volume":"2020","author":"Tallei","year":"2020","journal-title":"Scientifica"},{"key":"B104","doi-asserted-by":"publisher","first-page":"e2208058119","DOI":"10.1073\/pnas.2208058119","article-title":"T cell and B cell antigen receptors share a conserved core transmembrane structure","volume":"119","author":"Ramesh","year":"2022","journal-title":"Proc Natl Acad Sci USA."},{"key":"B105","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1111\/j.1399-0039.2010.01550.x","article-title":"The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding","volume":"4","author":"van Hateren","year":"2010","journal-title":"Tissue Antigens."},{"key":"B106","doi-asserted-by":"publisher","first-page":"1838","DOI":"10.1110\/ps.9.9.1838","article-title":"Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles","volume":"9","author":"Schueler-Furman","year":"2000","journal-title":"Protein Sci."},{"key":"B107","doi-asserted-by":"publisher","first-page":"2709","DOI":"10.1074\/jbc.M109098200","article-title":"Ligand exchange of major histocompatibility complex class II proteins is triggered by H-bond donor groups of small molecules","volume":"277","author":"Falk","year":"2002","journal-title":"J Biol Chem."},{"key":"B108","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1111\/j.1600-065X.1999.tb01369.x","article-title":"Individual hydrogen bonds play a critical role in MHC class II:peptide interactions: implications for the dynamic aspects of class II trafficking and DM-mediated peptide exchange","volume":"172","author":"Sant","year":"1999","journal-title":"Immunol Rev."},{"key":"B109","doi-asserted-by":"publisher","first-page":"22268","DOI":"10.1021\/acsomega.3c00205","article-title":"The Realm of unconventional noncovalent interactions in proteins: their significance in structure and function","volume":"8","author":"Adhav","year":"2023","journal-title":"ACS Omega."},{"key":"B110","doi-asserted-by":"publisher","first-page":"125992","DOI":"10.1016\/j.vaccine.2024.05.040","article-title":"Experimental and molecular dynamics simulation studies on the physical properties of three HBc-VLP derivatives as nanoparticle protein vaccine candidates","volume":"42","author":"Luo","year":"2024","journal-title":"Vaccine."},{"key":"B111","doi-asserted-by":"publisher","first-page":"7482","DOI":"10.1038\/s41598-019-44013-9","article-title":"Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance","volume":"9","author":"Khan","year":"2019","journal-title":"Sci Rep."},{"key":"B112","doi-asserted-by":"publisher","first-page":"24274","DOI":"10.1021\/acsomega.2c01475","article-title":"Protein model quality estimation using molecular dynamics simulation","volume":"7","author":"Kurniawan","year":"2022","journal-title":"ACS Omega."},{"key":"B113","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1186\/s40364-020-00228-x","article-title":"Roles of IFN-\u03b3 in tumor progression and regression: a review","volume":"8","author":"Jorgovanovic","year":"2020","journal-title":"Biomark Res."},{"key":"B114","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/nri3156","article-title":"The role of interleukin-2 during homeostasis and activation of the immune system","volume":"12","author":"Boyman","year":"2012","journal-title":"Nat Rev Immunol."},{"key":"B115","doi-asserted-by":"publisher","first-page":"575597","DOI":"10.3389\/fimmu.2020.575597","article-title":"Localized interleukin-12 for cancer immunotherapy","volume":"11","author":"Nguyen","year":"2020","journal-title":"Front Immunol."},{"key":"B116","first-page":"47","article-title":"Interferon and major histocompatibility complex genes: a model to analyse eukaryotic gene regulation?","volume":"7","author":"Rosa","year":"1986","journal-title":"Interferon."},{"key":"B117","doi-asserted-by":"publisher","first-page":"1210","DOI":"10.4049\/jimmunol.143.4.1210","article-title":"IL-2 and IFN-gamma are two necessary lymphokines in the development of cytolytic T cells","volume":"143","author":"Maraskovsky","year":"1989","journal-title":"J Immunol"},{"key":"B118","doi-asserted-by":"publisher","first-page":"2113","DOI":"10.1084\/jem.164.6.2113","article-title":"Gamma interferon enhances macrophage transcription of the tumor necrosis factor\/cachectin, interleukin 1, and urokinase genes, which are controlled by short-lived repressors","volume":"164","author":"Collart","year":"1986","journal-title":"J Exp Med."},{"key":"B119","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1016\/j.immuni.2008.03.003","article-title":"Contextual regulation of inflammation: a duet by transforming growth factor-beta and interleukin-10","volume":"4","author":"Li","year":"2008","journal-title":"Immunity."},{"key":"B120","doi-asserted-by":"publisher","first-page":"13618","DOI":"10.1038\/s41598-022-17950-1","article-title":"Anti-tumor activity of a T-helper 1 multiantigen vaccine in a murine model of prostate cancer","volume":"12","author":"Cecil","year":"2022","journal-title":"Sci Rep."},{"key":"B121","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1021\/acs.chemrev.9b00472","article-title":"Peptide-based vaccines: current progress and future challenges","volume":"120","author":"Malonis","year":"2019","journal-title":"Chem Rev."},{"key":"B122","doi-asserted-by":"publisher","first-page":"3016","DOI":"10.3390\/ijms11083016","article-title":"Advances and challenges in protein-ligand docking","volume":"11","author":"Huang","year":"2010","journal-title":"Int J Mol Sci."},{"key":"B123","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1017\/S0033583512000066","article-title":"Protein flexibility in docking and surface mapping","volume":"45","author":"Lexa","year":"2012","journal-title":"Q Rev Biophys."},{"key":"B124","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1186\/1741-7007-9-71","article-title":"Molecular dynamics simulations and drug discovery","volume":"9","author":"Durrant","year":"2011","journal-title":"BMC Biol."},{"key":"B125","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1016\/j.csbj.2019.07.010","article-title":"Applications of molecular dynamics simulation in structure prediction of peptides and proteins","volume":"17","author":"Geng","year":"2019","journal-title":"Comput Struct Biotechnol J."},{"key":"B126","doi-asserted-by":"publisher","first-page":"101324","DOI":"10.1016\/j.mam.2024.101324","article-title":"Cancer vaccines: target antigens, vaccine platforms and preclinical models","volume":"101","author":"Ruzzi","year":"2024","journal-title":"Mol Aspects Med."},{"key":"B127","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1007\/s00262-022-03245-x","article-title":"Preclinical development of a vaccine-based immunotherapy regimen (VBIR) that induces potent and durable T cell responses to tumor-associated self-antigens","volume":"72","author":"Cho","year":"2022","journal-title":"Cancer Immunol Immunother."}],"updated-by":[{"DOI":"10.3389\/fmed.2026.1824612","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:00:00Z","timestamp":1778198400000}}],"container-title":["Frontiers in Medicine"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmed.2026.1716345\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T13:27:14Z","timestamp":1778246834000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmed.2026.1716345\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,5]]},"references-count":127,"alternative-id":["10.3389\/fmed.2026.1716345"],"URL":"https:\/\/doi.org\/10.3389\/fmed.2026.1716345","relation":{},"ISSN":["2296-858X"],"issn-type":[{"value":"2296-858X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,5]]},"article-number":"1716345"}}