Multi-Epitope Vaccines
Multi-epitope vaccines, designed using the Reverse Vaccinology approach, represent a novel bioinformatics-based strategy for protein vaccine design that focuses on identifying, screening, and combining multiple immunogenic epitopes from one or more target antigens.[1]. In this approach, instead of using the entire antigen, only regions that play a key role in activating the immune system are selected[2]. After an antigen enters the body, antigen-presenting cells (APCs) process the antigen and present its immunogenic fragments, known as epitopes, on major histocompatibility complex (MHC) class I and class II molecules[3][4]. This process leads to the recognition of the epitope–MHC complex by T cells and the initiation of a cellular immune response. Activation of B lymphocytes, with the help of T cells, also results in the production of specific antibodies against the target epitopes[5].
In the design of multi-epitope vaccines, the antigen or antigens associated with the disease are first identified, which are often proteins[6][7]. Suitable epitopes are then selected based on criteria such as immunogenicity, population coverage, and other immunological factors[8]. These epitopes are linked together using flexible linkers and typically form a single chimeric protein structure, often combined with an adjuvant to enhance the immune response[9][10].
In the final stage, the vaccine construct is evaluated in terms of its primary structure (amino acid sequence), secondary structure, and tertiary structure. These assessments are performed using computational methods and established criteria to determine whether the designed construct can successfully meet stability and bioavailability requirements. If the results of these analyses are satisfactory, the construct is proposed as a multi-epitope vaccine candidate[11][12].
History
Computational and reverse vaccinology, which involves vaccine design based on pathogen genome analysis, was first introduced by Rino Rappuoli in the early 1990s[13]. This approach utilizes computational and bioinformatics tools to identify suitable antigens, significantly reducing both the time and cost of vaccine development[14].
One of the first major applications of reverse vaccinology was the study of Neisseria meningitidis serogroup B to develop a new subunit vaccine. This study, conducted in 2000, relied on the complete genome analysis of the microorganism using bioinformatics tools[15].
Although the field did not gain widespread attention initially, its significance increased markedly with the onset of the COVID-19 pandemic, which created an urgent need for rapid vaccine development. As a result, computational approaches, particularly the design of multi-epitope vaccines, have become an active and prominent area of research in modern vaccine development.[16][17]
Main steps in designing a multi-epitope vaccine
Step 1: Identification of the antigen or biomarker specific to the target disease
Identification of suitable antigens can be performed using various approaches. One of the simplest methods is to review the scientific literature and select antigens that have previously been identified as immunogenic targets in the disease of interest[18][19][20].
Another approach involves analysis of the pathogen genome and is mainly used in the design of vaccines against viruses, bacteria, and parasites. In this method, all protein-coding regions (open reading frames, ORFs) in the genome are first identified. These regions, which are capable of being translated into proteins, are then examined as potential antigens. ORFs typically begin with a start codon and end with a stop codon. The identified potential antigens are subsequently evaluated using various computational filters. Candidates that do not meet the required criteria are eliminated, while those with a high probability of inducing an immune response and suitable vaccine properties are advanced to the next stage [21][22]. Important criteria in selecting a suitable antigen include the following:
- Cellular location: Antigens located on the cell surface or outside the membrane (extracellular or outer membrane proteins) are generally more accessible to the immune system[23][24]
- Dissimilarity to host proteins: Antigens that are highly similar to human or animal host proteins may lead to reduced immunogenicity or potential cross-reactivity[25].
- Non-toxic and non-allergenic properties: Selected antigens should not be toxic or allergenic[26][27].
Finally, antigens that successfully pass all computational filters are ranked based on their predicted immunogenicity, and the best candidate is selected as the target antigen[28].
A third approach for identifying disease-specific antigens or biomarkers is commonly applied in cancer vaccine design and focuses on single-cell analysis. Using gene expression data from multiple cells derived from healthy and cancer populations, target cells and genes can be identified and included in the analysis after appropriate preprocessing. Cells are clustered, and gene expression patterns in both groups are compared to identify different cell types. By comparing similar cell populations between healthy and cancer samples, cancer-specific cells can be distinguished. Subsequently, genes encoding surface proteins that are highly expressed in these cancer cells are examined to identify proteins most likely present on the cell surface as potential antigens, provided that additional computational evaluations also support their suitability[29].
At the end of this step, the antigen or antigens specific to the target disease are determined, completing the first phase of vaccine design [30][31][32].
Step 2: Epitope identification and vaccine design
After the target antigen has been identified, the next step involves identifying immunogenic epitopes within the selected antigen. Today, this process is performed using various computational tools, with the primary objective of selecting the most suitable epitopes from all predicted candidates[33].
Epitopes are generally divided into two categories: linear and conformational (discontinuous). Linear epitopes consist of continuous sequences of amino acids in the primary structure of the protein, and their identification is usually based on the protein sequence. These epitopes can be recognized by the immune system even after the protein has been denatured and are therefore most commonly used in the prediction of T-cell epitopes and certain B-cell epitopes. In contrast, conformational epitopes are composed of non-contiguous amino acids in the primary sequence that are brought into proximity through the three-dimensional folding of the protein. Identification of these epitopes depends on the three-dimensional structure of the protein and is generally more important in the prediction of B-cell epitopes recognized by antibodies[34].
To select suitable epitopes, predicted candidates are evaluated using a set of computational filters. Important criteria include non-toxicity and non-allergenicity, ensuring that toxic or potentially allergenic epitopes are eliminated at an early stage[35]. Another key criterion is epitope conservation; particularly in pathogens with multiple strains, epitopes conserved across several strains are given higher priority [13]. In addition, population coverage is assessed to determine the proportion of the target population that can genetically respond to each epitope[36][37][38].
In addition to the basic criteria, other features are commonly used to evaluate and select epitopes for vaccine design[39]:
| Feature / Application Filter | Purpose / Description |
| Topology[40] | Determines the location of the epitope on the protein (surface or internal) |
| IL-4[41] | Predicts the epitope's ability to induce interleukin 4, supporting the immune response |
| IL-10[42] | Predicts the epitope's ability to induce interleukin 10, which helps control inflammation |
| IFN-γ[43] | Predicts induction of interferon gamma, important for cellular immune response |
| Water solubility[44] | Assesses the solubility of the epitope for vaccine production |
| MHC binding (IC50 / allele) [45] | Predicts the binding strength of the epitope to MHC molecules and the corresponding alleles |
| Immunogenicity[46] | Evaluates the ability of the epitope to induce an immune response |
| IgG / IgE / IgA score[47] | Predicts the capacity to induce various antibodies and the likelihood of allergic reactions |
| Hydrophobicity / Hydrophilicity / GRAVY [47] | Examines physicochemical properties and surface accessibility of the epitope |
| Molecular weight[48] | Determines epitope size for production and synthesis |
| Human homology[49] | Checks similarity with human proteins to reduce the risk of autoimmunity |
| Glycan-site[50] | Identifies glycosylation sites that may limit epitope accessibility |
| Ellipro score[51] | Predicts spatial B-cell epitopes based on 3D protein structure |
| Instability index [33] | Predicts epitope stability |
| Charge [52] | Evaluates the electrical charge of the epitope, important for accessibility and solubility |
Epitopes that successfully pass all computational filters are then ranked based on their immunogenicity, and the top candidates are selected for vaccine design. After selecting the epitopes, a multi-epitope vaccine construct is designed by linking them together using flexible linkers and incorporating an adjuvant. An adjuvant is a substance that enhances the immune system's response to an antigen and is typically included to improve vaccine efficacy[53].
Step 3: Evaluation and validation of the designed vaccine candidate
In computational multi-epitope vaccine design, constructs are commonly evaluated through a series of in silico analyses to assess their physicochemical properties, structural stability, and predicted immunogenicity. These evaluations typically include analysis of the primary structure (amino acid composition and molecular properties), secondary structure prediction, and tertiary structure modeling. Constructs that satisfy predefined criteria in these assessments may be proposed as potential vaccine candidates, subject to further experimental validation [54][55].
Evaluation of the primary structure
At this stage, the protein sequence of the vaccine is analyzed from multiple perspectives. Key criteria include non-toxicity and non-allergenicity, ensuring the sequence is safe for use[56][45]. The immunogenicity of the sequence is also assessed, along with physicochemical properties such as molecular weight, half-life, and overall protein stability[52][57].
Evaluation of the secondary structure
The secondary structure of the vaccine protein is predicted using computational tools, and the composition of structural elements, such as alpha helices and beta sheets, is analyzed. Features of the secondary structure can influence both the stability and immunogenicity of the construct[58][59].
Evaluation of the tertiary structure
The tertiary structure of the predicted protein and its structural quality are examined in detail. This includes stereochemical analyses, Ramachandran plot evaluation, and assessment of non-bonded interactions within the protein structure[60][61]. In addition to structural evaluations, molecular docking and molecular dynamics simulations are employed to investigate how the vaccine candidate interacts with components of the immune system. Molecular docking provides an initial assessment of binding affinity by predicting interaction states and energies, while molecular dynamics simulations analyze the temporal behavior of these complexes, assessing the stability and structural changes of interactions under near-physiological conditions[62][63].
Bioinformatics tools for multi-epitope vaccine design
In the design of multi-epitope vaccines, a wide range of bioinformatics tools are used to identify antigens, predict epitopes, and evaluate the structural properties of the vaccine construct. The following table summarizes commonly used tools and their applications:
| Tool | Application / Stage | Reference |
| Violinet | Literature review | [64] |
| ORF Finder | ORF identification | [65] |
| NCBI Genome Datasets | Genome analysis | [66] |
| PSORTb | Subcellular localization | [67] |
| Cell-PLoc | Subcellular localization | [68] |
| Blast | Non-homology to host proteins | [69] |
| ToxinPred | Toxicity prediction | [70] |
| AlgPred | Allergenicity prediction | [71] |
| AllerTOP | Allergenicity prediction | [72] |
| VaxiJen | Antigenicity prediction | [73] |
| IEDB | Epitope identification | [74] |
| ProtParam | Physicochemical property analysis | [75] |
| PSIPRED | Secondary structure prediction | [76] |
| JPred4 | Secondary structure prediction | [77] |
| GOR V | Secondary structure prediction | [78] |
| AlphaFold | 3D structural prediction | [79] |
| SWISS-MODEL | 3D structural modeling | [80] |
| I-TASSER | 3D structural prediction | [81] |
| ERRAT | 3D structural validation | [82] |
| PDBsum | Structural analysis | [83] |
| SwissDock | Molecular docking | [84] |
| ClusPro | Molecular docking | [85] |
| AutoDock | Molecular docking | [86] |
| GROMACS | Molecular dynamics simulation | [87] |
| iMODS | Molecular dynamics / flexibility analysis | [88] |
Challenges
The multi-epitope vaccine approach is an emerging strategy in vaccine design and faces several challenges. This approach primarily focuses on identifying protein antigens capable of being translated into proteins and extracting epitopes, which means that non-protein antigens, some of which may be highly relevant, are often overlooked. Additionally, the prediction of open reading frames (ORFs) and protein sequences is not always accurate; even a single codon shift can lead to incorrect sequences, which may arise during sequencing or subsequent analyses [89][90]
Despite advances in artificial intelligence and bioinformatics tools, predictions of protein properties, including immunogenicity and toxicity, are not always reliable. Computational filters may inadvertently exclude or mis-evaluate some potential candidates. Moreover, the potential synergistic effects of combining multiple proteins are often underexplored. Proteins with lower individual rankings could become effective vaccine components when combined with suitable adjuvants, yet they are frequently eliminated during the selection process.[91][14]
To address these limitations, many studies need to place greater emphasis on experimental immunology. In vitro and in vivo evaluations should be considered an integral part of multi-epitope vaccine development. Achieving this goal requires stronger interdisciplinary collaboration between bioinformatics, immunology, laboratory research, and the pharmaceutical industry. To increase the effectiveness and practical applicability of multi-epitope vaccines, computational approaches should be integrated with laboratory and preclinical studies, and effective communication between computational, experimental, and industrial research teams should be established from the earliest stages of design[92]
References
- ↑ Basmenj, Esmaeil Roohparvar; Pajhouh, Susan Radman; Ebrahimi Fallah, Afsane; naijian, Rafe; Rahimi, Elmira; Atighy, Hossein; Ghiabi, Shadan; Ghiabi, Shamim (January 2025). "Computational epitope-based vaccine design with bioinformatics approach; a review". Heliyon. 11 (1): e41714. Bibcode:2025Heliy..1141714B. doi:10.1016/j.heliyon.2025.e41714. ISSN 2405-8440. PMC 11761309 Check
|pmc=value (help). PMID 39866399 Check|pmid=value (help). - ↑ Chen, Xiaowei; Li, Yongfeng; Wang, Xiao (20 December 2024). "Multi-epitope vaccines: a promising strategy against viral diseases in swine". Frontiers in Cellular and Infection Microbiology. 14. doi:10.3389/fcimb.2024.1497580. ISSN 2235-2988. PMC 11695243 Check
|pmc=value (help). PMID 39760092 Check|pmid=value (help). Unknown parameter|article-number=ignored (help) - ↑ Ung, Trevor; Rutledge, Nakisha S.; Weiss, Adam M.; Esser-Kahn, Aaron P.; Deak, Peter (16 August 2023). "Cell-targeted vaccines: implications for adaptive immunity". Frontiers in Immunology. 14. doi:10.3389/fimmu.2023.1221008. ISSN 1664-3224. PMC 10468591 Check
|pmc=value (help). PMID 37662903 Check|pmid=value (help). Unknown parameter|article-number=ignored (help) - ↑ Song, Xin; Li, Yongfeng; Wu, Hongxia; Qiu, Hua-Ji; Sun, Yuan (17 October 2024). "T-Cell Epitope-Based Vaccines: A Promising Strategy for Prevention of Infectious Diseases". Vaccines. 12 (10): 1181. doi:10.3390/vaccines12101181. ISSN 2076-393X. PMC 11511246 Check
|pmc=value (help). PMID 39460347 Check|pmid=value (help). - ↑ Melgoza-González, Edgar Alonso; Bustamante-Córdova, Lorena; Hernández, Jesús (10 March 2023). "Recent advances in antigen targeting to antigen-presenting cells in veterinary medicine". Frontiers in Immunology. 14. doi:10.3389/fimmu.2023.1080238. ISSN 1664-3224. PMC 10038197 Check
|pmc=value (help). PMID 36969203 Check|pmid=value (help). Unknown parameter|article-number=ignored (help) - ↑ Li, Zewei; Chen, Yifei; Xie, Haiping; Li, Quan; Wang, Shifeng; Shi, Huoying (1 December 2024). "Identification of immunogenic antigens and evaluation of vaccine candidates against Clostridium perfringens". Poultry Science. 103 (12): 104436. doi:10.1016/j.psj.2024.104436. ISSN 0032-5791. PMC 11550177 Check
|pmc=value (help). PMID 39467405 Check|pmid=value (help). - ↑ Clemente-Suárez, Vicente Javier; Redondo-Flórez, Laura; Bustamante-Sánchez, Alvaro; Martín-Rodríguez, Alexandra; Yáñez-Sepúlveda, Rodrigo; Tornero-Aguilera, Jose Francisco (3 July 2025). "Biometric Strategies to Improve Vaccine Immunogenicity and Effectiveness". Biomimetics. 10 (7): 439. doi:10.3390/biomimetics10070439. ISSN 2313-7673. PMC 12292147 Check
|pmc=value (help). PMID 40710252 Check|pmid=value (help). - ↑ Villanueva-Flores, Francisca; Sanchez-Villamil, Javier I.; Garcia-Atutxa, Igor (30 August 2025). "AI-driven epitope prediction: a systematic review, comparative analysis, and practical guide for vaccine development". npj Vaccines. 10 (1): 207. doi:10.1038/s41541-025-01258-y. ISSN 2059-0105. PMC 12398602 Check
|pmc=value (help). PMID 40885731 Check|pmid=value (help). - ↑ Facciolà, Alessio; Visalli, Giuseppa; Laganà, Antonio; Di Pietro, Angela (22 May 2022). "An Overview of Vaccine Adjuvants: Current Evidence and Future Perspectives". Vaccines. 10 (5): 819. doi:10.3390/vaccines10050819. ISSN 2076-393X. PMC 9147349 Check
|pmc=value (help). PMID 35632575 Check|pmid=value (help). - ↑ Cernuto, Federica; Maleki, Avisa; Russo, Giulia; Di Salvatore, Valentina; Pappalardo, Francesco (2 December 2025). "In-silico epitope-based vaccines design: progress, challenges and the road ahead". Expert Opinion on Drug Discovery. 20 (12): 1701–1712. doi:10.1080/17460441.2025.2599178. ISSN 1746-0441. PMID 41354625 Check
|pmid=value (help). - ↑ Qiu, Jingxuan; Wei, Yiwen; Shu, Jiayi; Zheng, Wenjing; Zhang, Yuxi; Xie, Junting; Zhang, Dong; Luo, Xiaochuan; Sun, Xiulan; Wang, Xin; Wang, Sijie; Wang, Xuanyi; Qiu, Tianyi (27 May 2025). "Integrated in-silico design and in vivo validation of multi-epitope vaccines for norovirus". Virology Journal. 22 (1): 166. doi:10.1186/s12985-025-02796-6. ISSN 1743-422X. PMC 12117790 Check
|pmc=value (help). PMID 40426240 Check|pmid=value (help). - ↑ Basmenj, Esmaeil Roohparvar; Arastonejad, Mahshid; Mamizadeh, Mina; Alem, Mahsa; KhalatbariLimaki, Mahdi; Ghiabi, Shadan; Khamesipour, Ali; Majidiani, Hamidreza; Shams, Morteza; Irannejad, Hamid (8 November 2023). "Engineering and design of promising T-cell-based multi-epitope vaccine candidates against leishmaniasis". Scientific Reports. 13 (1): 19421. Bibcode:2023NatSR..1319421B. doi:10.1038/s41598-023-46408-1. ISSN 2045-2322. PMC 10632461 Check
|pmc=value (help). PMID 37940672 Check|pmid=value (help). - ↑ Rappuoli, Rino (1 October 2000). "Reverse vaccinology". Current Opinion in Microbiology. 3 (5): 445–450. doi:10.1016/S1369-5274(00)00119-3. ISSN 1369-5274. PMID 11050440.
- ↑ 14.0 14.1 Alashwal, Hany; Kochunni, Nishi Palakkal; Hayawi, Kadhim (1 January 2025). "Application of machine learning and deep learning techniques on reverse vaccinology – a systematic literature review". Soft Computing. 29 (1): 391–403. doi:10.1007/s00500-025-10480-8. ISSN 1433-7479.
- ↑ "Science". AAAS. doi:10.1126/science.287.5459.1816. Retrieved 21 February 2026.
- ↑ Goodswen, Stephen J; Kennedy, Paul J; Ellis, John T (10 March 2023). "A guide to current methodology and usage of reverse vaccinology towards in silico vaccine discovery". FEMS Microbiology Reviews. 47 (2). doi:10.1093/femsre/fuad004. ISSN 1574-6976. PMID 36806618 Check
|pmid=value (help). Unknown parameter|article-number=ignored (help) - ↑ Rappuoli, Rino; De Gregorio, Ennio; Del Giudice, Giuseppe; Phogat, Sanjay; Pecetta, Simone; Pizza, Mariagrazia; Hanon, Emmanuel (19 January 2021). "Vaccinology in the post−COVID-19 era". Proceedings of the National Academy of Sciences. 118 (3): e2020368118. Bibcode:2021PNAS..11820368R. doi:10.1073/pnas.2020368118. PMC 7826410 Check
|pmc=value (help). PMID 33431690 Check|pmid=value (help). - ↑ Roohparvar Basmenj, Esmaeil; Omidvar, Behnoosh; Kiumarsy, Armity; Izadkhah, Habib; Ghiabi, Shamim (12 October 2024). "Design of a multi-epitope-based peptide vaccine against the SARS-CoV-2 Omicron variant using bioinformatics approach". Journal of Biomolecular Structure and Dynamics. 42 (15): 7945–7956. doi:10.1080/07391102.2023.2241926. ISSN 0739-1102. PMID 37539837 Check
|pmid=value (help). - ↑ Kordi, Bahareh; Basmenj, Esmaeil Roohparvar; Majidiani, Hamidreza; Basati, Gholam; Sargazi, Dariush; Nazari, Naser; Shams, Morteza (January 2023). Shivahare, Rahul, ed. "In Silico Characterization of an Important Metacyclogenesis Marker in Leishmania donovani , HASPB1, as a Potential Vaccine Candidate". BioMed Research International. 2023 (1). doi:10.1155/2023/3763634. ISSN 2314-6133. PMC 10266922 Check
|pmc=value (help). PMID 37323936 Check|pmid=value (help). Unknown parameter|article-number=ignored (help) - ↑ Zahraei, Mohammad; Roohparvar Basmenj, Esmaeil; Behrouzi, Gholamreza; Heidari Keshel, Saeed; Alem, Mahsa (27 November 2025). "In silico design of a multi-epitope vaccine against the triple negative breast cancer". Scientific Reports. 15 (1): 42425. Bibcode:2025NatSR..1542425Z. doi:10.1038/s41598-025-26511-1. ISSN 2045-2322. PMC 12660892 Check
|pmc=value (help). PMID 41309872 Check|pmid=value (help). - ↑ Roohparvar Basmenj, Esmaeil; Izadkhah, Habib; Hosseinpour, Maryam; Saburi, Ehsan; Abhaji Ezabadi, Marjan; Alipourfard, Iraj (20 December 2024). "A novel approach to design a multiepitope peptide as a vaccine candidate for Bordetella pertussis". Journal of Biomolecular Structure and Dynamics. 42 (24): 13738–13750. doi:10.1080/07391102.2023.2278081. ISSN 0739-1102. PMID 37937610 Check
|pmid=value (help). - ↑ Koupaei, Fatemeh Nouri; Kiumarsy, Armity; Feizi, Mohammad Mahdi; Vajdi, Zohreh; Edalat Pishkar, Seyed; Alem, Mahsa; Roohparvar Basmenj, Esmaeil (1 April 2025). "Design of a multi-epitope vaccine candidate against Vibrio cholerae". Scientific Reports. 15 (1): 11033. Bibcode:2025NatSR..1511033K. doi:10.1038/s41598-025-90598-9. ISSN 2045-2322. PMC 11958690 Check
|pmc=value (help). PMID 40164630 Check|pmid=value (help). - ↑ Rawal, Kamal; Sinha, Robin; Abbasi, Bilal Ahmed; Chaudhary, Amit; Nath, Swarsat Kaushik; Kumari, Priya; Preeti, P.; Saraf, Devansh; Singh, Shachee; Mishra, Kartik; Gupta, Pranjay; Mishra, Astha; Sharma, Trapti; Gupta, Srijanee; Singh, Prashant (2 September 2021). "Identification of vaccine targets in pathogens and design of a vaccine using computational approaches". Scientific Reports. 11 (1): 17626. Bibcode:2021NatSR..1117626R. doi:10.1038/s41598-021-96863-x. ISSN 2045-2322. PMC 8413327 Check
|pmc=value (help). PMID 34475453 Check|pmid=value (help). - ↑ Leow, Chiuan Yee; Kazi, Ada; Hisyam Ismail, Che Muhammad Khairul; Chuah, Candy; Lim, Boon Huat; Leow, Chiuan Herng; Banga Singh, Kirnpal Kaur (1 January 2020). "Reverse vaccinology approach for the identification and characterization of outer membrane proteins of Shigella flexneri as potential cellular- and antibody-dependent vaccine candidates". Clinical and Experimental Vaccine Research. 9 (1): 15–25. doi:10.7774/cevr.2020.9.1.15. ISSN 2287-3651. PMC 7024733 Check
|pmc=value (help). PMID 32095437 Check|pmid=value (help). - ↑ Tombari, Wafa; Khamessi, Oussema; Othman, Houcemeddine; Kallala, Ouafa; Mahjoub, Rihab; Ghedira, Kais; Trabelsi, Abdelhalim (19 August 2025). "A novel mRNA-based multi-epitope vaccine for rabies virus computationally designed via reverse vaccinology and immunoinformatics". Scientific Reports. 15 (1): 30355. Bibcode:2025NatSR..1530355T. doi:10.1038/s41598-025-16143-w. ISSN 2045-2322. PMC 12365161 Check
|pmc=value (help). PMID 40830404 Check|pmid=value (help). - ↑ Zubair, Akmal; Ali, Muhammad; Al-Emam, Ahmed; Elmagzoub, Ranya Mohammed (29 September 2025). "Integrative genomic and immunoinformatic approach for characterizing HIV-1 pol, vpr, and Nef genes and designing a multi-epitope vaccine". Scientific Reports. 15 (1): 33690. Bibcode:2025NatSR..1533690Z. doi:10.1038/s41598-025-18828-8. ISSN 2045-2322. PMC 12480126 Check
|pmc=value (help). PMID 41023018 Check|pmid=value (help). - ↑ Luo, Jia-Rui; Qi, Xin-Xin; Tian, Ting-Ting; Shang, Kai-Yu; Shi, Hui-Dong; Li, Chuang; Chai, Zheng-Long; Ding, Jian-Bing; Zhu, Yue-Jie; Zhang, Feng-Bo (21 August 2025). "Design of a multi-Epitope mRNA vaccine against Brucella type IV secretion system using reverse vaccinology and immunogenicity approaches". Scientific Reports. 15 (1): 30698. Bibcode:2025NatSR..1530698L. doi:10.1038/s41598-025-09509-7. ISSN 2045-2322. PMC 12370932 Check
|pmc=value (help). PMID 40841725 Check|pmid=value (help). - ↑ Li, Shinian; Yu, Jingjing; Xiao, Chencheng; Li, Yaling (29 March 2025). "Immunoinformatics method to design universal multi-epitope nanoparticle vaccine for TGEV S protein". Scientific Reports. 15 (1): 10931. Bibcode:2025NatSR..1510931L. doi:10.1038/s41598-025-95602-w. ISSN 2045-2322. PMC 11954851 Check
|pmc=value (help). PMID 40158011 Check|pmid=value (help). - ↑ Nguyen, Hong Nhi; Vanderzee, Isabel O.; Wen, Fei (26 June 2025). "The Application of Single-Cell Technologies for Vaccine Development Against Viral Infections". Vaccines. 13 (7): 687. doi:10.3390/vaccines13070687. ISSN 2076-393X. PMC 12300521 Check
|pmc=value (help). PMID 40733664 Check|pmid=value (help). - ↑ Rappuoli, Rino; Bottomley, Matthew J.; D'Oro, Ugo; Finco, Oretta; De Gregorio, Ennio (4 April 2016). "Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design". Journal of Experimental Medicine. 213 (4): 469–481. doi:10.1084/jem.20151960. ISSN 0022-1007. PMC 4821650. PMID 27022144.
- ↑ Gloanec, Noémie; Guyard-Nicodème, Muriel; Chemaly, Marianne; Dory, Daniel (27 February 2025). "Reverse vaccinology: A strategy also used for identifying potential vaccine antigens in poultry". Vaccine. 48. doi:10.1016/j.vaccine.2025.126756. ISSN 0264-410X. PMID 39855107 Check
|pmid=value (help). Unknown parameter|article-number=ignored (help) - ↑ Rao, Dharmendrasinh F.; Patel, Saumya K.; Pandya, Himanshu A. (30 September 2025). "Immunoinformatics-guided vaccine design: A review with case study on Marburg virus". Biochemical and Biophysical Research Communications. 782. Bibcode:2025BBRC..782o2572R. doi:10.1016/j.bbrc.2025.152572. ISSN 0006-291X. PMID 40907270 Check
|pmid=value (help). Unknown parameter|article-number=ignored (help) - ↑ 33.0 33.1 Sharma, Arijit Das; Magdaleno, Jorge Samuel Leon; Singh, Himanshu; Orduz, Andrés Felipe Cuspoca; Cavallo, Luigi; Chawla, Mohit (7 April 2025). "Immunoinformatics-driven design of a multi-epitope vaccine targeting neonatal rotavirus with focus on outer capsid proteins VP4 and VP7 and non structural proteins NSP2 and NSP5". Scientific Reports. 15 (1): 11879. Bibcode:2025NatSR..1511879S. doi:10.1038/s41598-025-95256-8. ISSN 2045-2322. PMC 11976959 Check
|pmc=value (help). PMID 40195509 Check|pmid=value (help). - ↑ Li, Jing; Ju, Yan; Jiang, Min; Li, Sha; Yang, Xiao-Yan (27 February 2025). "Epitope-Based Vaccines: The Next Generation of Promising Vaccines Against Bacterial Infection". Vaccines. 13 (3): 248. doi:10.3390/vaccines13030248. ISSN 2076-393X. PMC 11946261 Check
|pmc=value (help). PMID 40266107 Check|pmid=value (help). - ↑ Deepthi, Varughese; Sasikumar, Aswathy; Mohanakumar, Kochupurackal P.; Rajamma, Usha (20 March 2025). "Computationally designed multi-epitope vaccine construct targeting the SARS-CoV-2 spike protein elicits robust immune responses in silico". Scientific Reports. 15 (1): 9562. Bibcode:2025NatSR..15.9562D. doi:10.1038/s41598-025-92956-z. ISSN 2045-2322. PMC 11923050 Check
|pmc=value (help). PMID 40108271 Check|pmid=value (help). - ↑ Wang, Yimeng; Galkin, Andrey; Shang, Xiaoran; Marin, Alexander; Jin, Shaohua; Ye, Ting-Juan; Bale, Shridhar; Chiang, Chi-I.; Chowdhury, Ananda; Chenine, Agnes L.; Turonis, Ashley; Greenhouse, Jack; Stone, Rebecca; Wear, Jaclyn; Kar, Swagata (22 December 2025). "Rational design of flavivirus E protein vaccine optimizes immunogenicity and mitigates antibody dependent enhancement risk". Nature Communications. 16 (1): 11558. Bibcode:2025NatCo..1611558W. doi:10.1038/s41467-025-67447-4. ISSN 2041-1723. PMC 12748774 Check
|pmc=value (help). PMID 41429771 Check|pmid=value (help). - ↑ Lin, Ting-Hui; Lee, Chang-Chun David; Fernández-Quintero, Monica L.; Ferguson, James A.; Han, Julianna; Zhu, Xueyong; Yu, Wenli; Guthmiller, Jenna J.; Krammer, Florian; Wilson, Patrick C.; Ward, Andrew B.; Wilson, Ian A. (2 February 2025). "Structurally convergent antibodies derived from different vaccine strategies target the influenza virus HA anchor epitope with a subset of VH3 and VK3 genes". Nature Communications. 16 (1): 1268. doi:10.1038/s41467-025-56496-4. ISSN 2041-1723. PMC 11788443 Check
|pmc=value (help). PMID 39894881 Check|pmid=value (help). - ↑ Mashhadi Abolghasem Shirazi, Maryam; Hanan, Mina; Arashkia, Arash; Sadat, Seyed Mehdi (25 September 2025). "Novel bioinformatics approaches to design epitope-based vaccine against HIV latency by inquiring CTL epitopes and built-in adjuvants". Scientific Reports. 15 (1): 32809. Bibcode:2025NatSR..1532809M. doi:10.1038/s41598-025-17196-7. ISSN 2045-2322. PMC 12464155 Check
|pmc=value (help). PMID 40998947 Check|pmid=value (help). - ↑ Mortazavi, Behnam; Molaei, Ali; Fard, Najaf Allahyari (1 May 2024). "Multi-epitope vaccines, from design to expression; an in silico approach". Human Immunology. 85 (3): 110804. doi:10.1016/j.humimm.2024.110804. ISSN 0198-8859. PMID 38658216 Check
|pmid=value (help). - ↑ Mashrur, Md Nafij; Imranuzzaman, Md; Barua, Hridoy; Hasan, Md Rakibul; Hridy, Faria Khan; Sakib, Tasnim Sayem; Rani, Nurul Amin; Rahman, Mostafizor; Ahsan, Golam; Ashraf, Tanvir; Muktadir, Sofiur; Belal, Anika Binte; Roy, Apurba; Mohiuddin, A. S. M.; Shishir, Tushar Ahmed (26 November 2025). "In silico design of novel multi-epitope peptide vaccine against Neospora caninum induced cattle abortion targeting extracellular GRA2 and Nc-p43 protein". Scientific Reports. 15 (1): 42169. Bibcode:2025NatSR..1542169M. doi:10.1038/s41598-025-26139-1. ISSN 2045-2322. PMC 12658060 Check
|pmc=value (help). PMID 41298714 Check|pmid=value (help). - ↑ Mahafujul Alam, Syed Sahajada; Mir, Showkat Ahmad; Samanta, Arijit; Nayak, Binata; Ali, Safdar; Hoque, Mehboob (11 April 2025). "Immunoinformatics based designing of a multi-epitope cancer vaccine targeting programmed cell death ligand 1". Scientific Reports. 15 (1): 12420. Bibcode:2025NatSR..1512420M. doi:10.1038/s41598-025-87063-y. ISSN 2045-2322. PMC 11992185 Check
|pmc=value (help). PMID 40216819 Check|pmid=value (help). - ↑ Ma, Shiyang; Zhu, Fei; Zhang, Peipei; Xu, Yizhong; Zhou, Ziyou; Yang, Hang; Tan, Caixia; Chen, Jie; Pan, Pinhua (9 January 2025). "Development of a novel multi-epitope subunit mRNA vaccine candidate to combat Acinetobacter baumannii". Scientific Reports. 15 (1): 1410. Bibcode:2025NatSR..15.1410M. doi:10.1038/s41598-024-84823-0. ISSN 2045-2322. PMC 11718249 Check
|pmc=value (help). PMID 39789105 Check|pmid=value (help). - ↑ Razzak, Abdur; Ahmed, Firoz; Mahmud, Md Toslim (30 September 2025). "Development of a multi-epitope vaccine against Helicobacter pylori using a novel saRNA technology through an immunoinformatics approach". Scientific Reports. 15 (1): 33753. Bibcode:2025NatSR..1533753R. doi:10.1038/s41598-025-99512-9. ISSN 2045-2322. PMC 12484783 Check
|pmc=value (help). PMID 41028278 Check|pmid=value (help). - ↑ Zubair, Akmal; Ahmad, Faisal; Hussain, Syeda Maryam; Manzoor, Zahid; Al-Emam, Ahmed; Wdidi, Safa (17 December 2025). "Molecular assessment of the HIV pol gene and use of computational vaccine design targeting Pakistani isolates". Scientific Reports. 15 (1): 43984. Bibcode:2025NatSR..1543984Z. doi:10.1038/s41598-025-27720-4. ISSN 2045-2322. PMC 12711964 Check
|pmc=value (help). PMID 41407767 Check|pmid=value (help). - ↑ 45.0 45.1 Izhari, Mohammad Asrar; Gosady, Ahmed R. A.; Alghamdi, Fahad; Alghamdi, Wael A.; Hadadi, Mansour A. A.; Almontasheri, Ahmad H. A.; Dardari, Daifallah M. M.; Salem, Ahmad A.; Alotaibi, Foton E. (24 December 2025). "Rational design and in silico characterization of a multiepitope mRNA vaccine candidate against human metapneumovirus (hMPV) using reverse vaccinology and immunoinformatics approaches". Scientific Reports. 16 (1): 540. doi:10.1038/s41598-025-29906-2. ISSN 2045-2322. PMC 12774926 Check
|pmc=value (help). PMID 41444309 Check|pmid=value (help). - ↑ Allemailem, Khaled S.; Alrumaihi, Faris; Almatroudi, Ahmad (25 December 2025). "Immunoinformatics-based design of a next generation multi-epitope vaccine candidate against Shigella boydii using a hierarchical subtractive proteomics approach". Scientific Reports. 16 (1): 3359. doi:10.1038/s41598-025-33252-8. ISSN 2045-2322. PMC 12835280 Check
|pmc=value (help). PMID 41449186 Check|pmid=value (help). - ↑ 47.0 47.1 Akurut, Eva; Gavamukulya, Yahaya; Mulindwa, Julius; Isiagi, Moses; Galiwango, Ronald; Bbuye, Mudarshiru; Lujumba, Ibra; Kiberu, Davis; Nabisubi, Patricia; Kebirungi, Grace; Kambugu, Andrew; Castelnuovo, Barbara; Nkurunungi, Gyaviira; Jjingo, Daudi; Oketch, Brenda (26 July 2025). "Design of a multi-epitope vaccine against drug-resistant mycobacterium tuberculosis and mycobacterium bovis using reverse vaccinology". Scientific Reports. 15 (1): 27298. Bibcode:2025NatSR..1527298A. doi:10.1038/s41598-025-11768-3. ISSN 2045-2322. PMC 12297362 Check
|pmc=value (help). PMID 40715271 Check|pmid=value (help). - ↑ Shahriari-Namadi, Marziae; Azizi, Kourosh; Alipour, Hamzeh (24 July 2025). "In-silico study: Hm86 protein of Hyalomma marginatum (Ixodida) as a candidate to provide anti-tick vaccine". Scientific Reports. 15 (1): 27008. Bibcode:2025NatSR..1527008S. doi:10.1038/s41598-025-12871-1. ISSN 2045-2322. PMC 12289955 Check
|pmc=value (help). PMID 40707703 Check|pmid=value (help). - ↑ Sarvmeili, Javad; Baghban Kohnehrouz, Bahram; Gholizadeh, Ashraf; Shanehbandi, Dariush; Ofoghi, Hamideh (4 May 2024). "Immunoinformatics design of a structural proteins driven multi-epitope candidate vaccine against different SARS-CoV-2 variants based on fynomer". Scientific Reports. 14 (1): 10297. Bibcode:2024NatSR..1410297S. doi:10.1038/s41598-024-61025-2. ISSN 2045-2322. PMC 11069592 Check
|pmc=value (help). PMID 38704475 Check|pmid=value (help). - ↑ Naveed, Muhammad; Ali, Adeeba; Aziz, Tariq; Ali, Nouman; Rehman, Hafiz Muzzammel; Khan, Ayaz Ali; ul Haq, Taqweem; El Hadi Mohamed, Rania Ali; Al-Asmari, Fahad; Alwethaynani, Maher S.; Al-Joufi, Fakhria A.; Fallatah, Deema (22 April 2025). "Computational design of a glycosylated multi-epitope vaccine against HAsV-1 and HAsV-2 astrovirus for acute gastroenteritis". Scientific Reports. 15 (1): 13954. Bibcode:2025NatSR..1513954N. doi:10.1038/s41598-025-96989-2. ISSN 2045-2322. PMC 12015304 Check
|pmc=value (help). PMID 40263512 Check|pmid=value (help). - ↑ Shahraki, Parisa Kh; Kiani, Razie; Siavash, Mansour; Bemani, Peyman (25 April 2025). "Design of a multi-epitope vaccine against Staphylococcus Aureus lukotoxin ED using in silico approaches". Scientific Reports. 15 (1): 14517. Bibcode:2025NatSR..1514517S. doi:10.1038/s41598-025-85147-3. ISSN 2045-2322. PMC 12032201 Check
|pmc=value (help). PMID 40280948 Check|pmid=value (help). - ↑ 52.0 52.1 Aram, Cena; Karami, Leila; Ranjbar, Mohammad Mehdi (2 July 2025). "Development of a candidate mRNA vaccine based on Multi-Peptide targeting VP4 of rotavirus A: an immunoinformatics and molecular dynamics approach". Scientific Reports. 15 (1): 22610. Bibcode:2025NatSR..1522610A. doi:10.1038/s41598-025-07433-4. ISSN 2045-2322. PMC 12218802 Check
|pmc=value (help). PMID 40594603 Check|pmid=value (help). - ↑ Zhao, Tingmei; Cai, Yulong; Jiang, Yujie; He, Xuemei; Wei, Yuquan; Yu, Yifan; Tian, Xiaohe (19 July 2023). "Vaccine adjuvants: mechanisms and platforms". Signal Transduction and Targeted Therapy. 8 (1): 283. doi:10.1038/s41392-023-01557-7. ISSN 2059-3635. PMC 10356842 Check
|pmc=value (help). PMID 37468460 Check|pmid=value (help). - ↑ Maleki, Avisa; Russo, Giulia; Parasiliti Palumbo, Giuseppe Alessandro; Pappalardo, Francesco (2 February 2022). "In silico design of recombinant multi-epitope vaccine against influenza A virus". BMC Bioinformatics. 22 (14): 617. doi:10.1186/s12859-022-04581-6. ISSN 1471-2105. PMC 8808469 Check
|pmc=value (help). PMID 35109785 Check|pmid=value (help). - ↑ Tanner, Tayhlor; Medhavi, F N U; Richardson, Shakyra; Omosun, Yusuf O; Eko, Francis O (7 February 2024). "In silico design and analysis of a multiepitope vaccine against Chlamydia". Pathogens and Disease. 82. doi:10.1093/femspd/ftae015. ISSN 2049-632X. PMC 11234648 Check
|pmc=value (help). PMID 38889932 Check|pmid=value (help). Unknown parameter|article-number=ignored (help) - ↑ Hatamian, Ghazaleh; Ebrahimpour, Amirali; Nejabat, Mojgan; Hadizadeh, Farzin (24 November 2025). "Targeting SOX9: designing a novel vaccine against triple-negative breast cancer". Scientific Reports. 15 (1): 41553. Bibcode:2025NatSR..1541553H. doi:10.1038/s41598-025-25499-y. ISSN 2045-2322. PMC 12644569 Check
|pmc=value (help). PMID 41286148 Check|pmid=value (help). - ↑ Mirzaie, Sako; Yuan, Kevin Da; Ni, Heyu; Wu, Xiao Yu (5 July 2025). "Design of a novel multiepitope vaccine against glioblastoma by in silico approaches". Scientific Reports. 15 (1): 24046. Bibcode:2025NatSR..1524046M. doi:10.1038/s41598-025-03672-7. ISSN 2045-2322. PMC 12228682 Check
|pmc=value (help). PMID 40617889 Check|pmid=value (help). - ↑ Zaman, Naila; Gul, Kainat; Khurram, Kinza; Azam, Syed Sikander (1 July 2025). "Molecular insights into pangenome localization and constructs design for Hemophilus influenza vaccine". Scientific Reports. 15 (1): 22316. Bibcode:2025NatSR..1522316Z. doi:10.1038/s41598-025-03536-0. ISSN 2045-2322. PMC 12217137 Check
|pmc=value (help). PMID 40594015 Check|pmid=value (help). - ↑ Baneshi, Maryam; Sadeghi, Mahboubeh; Hashemi, Samaneh; Alcedo, Claudia; Muro, Antonio; Manzano-Román, Raúl; Savardashtaki, Amir; Rashidi, Sajad (10 November 2025). "Design of a novel multi epitope antigen for diagnosis of visceral leishmaniasis using an immunoinformatics approach". Scientific Reports. 15 (1): 39308. Bibcode:2025NatSR..1539308B. doi:10.1038/s41598-025-23012-z. ISSN 2045-2322. PMC 12603214 Check
|pmc=value (help). PMID 41214019 Check|pmid=value (help). - ↑ Ranjbar, Kimia Jafari; Sarkoohi, Parisa; Shahbazi, Behzad; Babaei, Maryam; Ahmadi, Khadijeh (1 March 2025). "Bioinformatics analysis of the in silico engineered protein vaccine with and without Escherichia coli heat labile enterotoxin adjuvant on the model of Klebsiella pneumoniae". Scientific Reports. 15 (1): 7321. Bibcode:2025NatSR..15.7321R. doi:10.1038/s41598-025-91602-y. ISSN 2045-2322. PMC 11873140 Check
|pmc=value (help). PMID 40025224 Check|pmid=value (help). - ↑ Adelusi, Temitope Isaac; Ogunlana, Abdeen Tunde; Oyewole, Moyosoluwa Precious; Ojo, Taiwo Ooreoluwa; Olaoba, Olamide Tosin; Oladipo, Elijah Kolawole; Akash, Shopnil; Ibenmoussa, Samir; Bourhia, Mohammed; Jardan, Yousef A. Bin; Sitotaw, Baye (20 January 2025). "Designing of an innovative conserved multiepitope subunit vaccine targeting SARS-CoV-2 glycoprotein and nucleoprotein through immunoinformatic". Scientific Reports. 15 (1): 2563. Bibcode:2025NatSR..15.2563A. doi:10.1038/s41598-024-72495-9. ISSN 2045-2322. PMC 11747174 Check
|pmc=value (help). PMID 39833186 Check|pmid=value (help). - ↑ Shetty, Seema; Dash, Swagatika; Kumar, Avinash; Vishwanath, Shashidhar; Kini, Suvarna G.; Brand, Angela (2 December 2024). "Immunoinformatics design of a multi-epitope vaccine for Chlamydia trachomatis major outer membrane proteins". Scientific Reports. 14 (1): 29919. Bibcode:2024NatSR..1429919S. doi:10.1038/s41598-024-81736-w. ISSN 2045-2322. PMC 11612408 Check
|pmc=value (help). PMID 39623035 Check|pmid=value (help). - ↑ Momajadi, Leila; Khanahmad, Hossein; Mahnam, Karim (25 October 2024). "Designing a multi-epitope influenza vaccine: an immunoinformatics approach". Scientific Reports. 14 (1): 25382. Bibcode:2024NatSR..1425382M. doi:10.1038/s41598-024-74438-w. ISSN 2045-2322. PMC 11512060 Check
|pmc=value (help). PMID 39455641 Check|pmid=value (help). - ↑ He, Yongqun; Racz, Rebecca; Sayers, Samantha; Lin, Yu; Todd, Thomas; Hur, Junguk; Li, Xinna; Patel, Mukti; Zhao, Boyang; Chung, Monica; Ostrow, Joseph; Sylora, Andrew; Dungarani, Priya; Ulysse, Guerlain; Kochhar, Kanika (January 2014). "Updates on the web-based VIOLIN vaccine database and analysis system". Nucleic Acids Research. 42 (D1): D1124–D1132. doi:10.1093/nar/gkt1133. ISSN 0305-1048. PMC 3964998. PMID 24259431.
- ↑ Rombel, Irene T; Sykes, Kathryn F; Rayner, Simon; Johnston, Stephen Albert (9 January 2002). "ORF-FINDER: a vector for high-throughput gene identification". Gene. 282 (1): 33–41. doi:10.1016/S0378-1119(01)00819-8. ISSN 0378-1119. PMID 11814675.
- ↑ O'Leary, Nuala A.; Cox, Eric; Holmes, J. Bradley; Anderson, W. Ray; Falk, Robert; Hem, Vichet; Tsuchiya, Mirian T. N.; Schuler, Gregory D.; Zhang, Xuan; Torcivia, John; Ketter, Anne; Breen, Laurie; Cothran, Jonathan; Bajwa, Hena; Tinne, Jovany (5 July 2024). "Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets". Scientific Data. 11 (1): 732. doi:10.1038/s41597-024-03571-y. ISSN 2052-4463. PMC 11226681 Check
|pmc=value (help). PMID 38969627 Check|pmid=value (help). - ↑ Nakai, Kenta; Horton, Paul (January 1999). "PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization". Trends in Biochemical Sciences. 24 (1): 34–35. doi:10.1016/S0968-0004(98)01336-X. ISSN 0968-0004. PMID 10087920.
- ↑ Chou, Kuo-Chen; Shen, Hong-Bin (February 2008). "Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms". Nature Protocols. 3 (2): 153–162. doi:10.1038/nprot.2007.494. ISSN 1750-2799. PMID 18274516.
- ↑ Altschul, Stephen F.; Gish, Warren; Miller, Webb; Myers, Eugene W.; Lipman, David J. (5 October 1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–410. doi:10.1016/S0022-2836(05)80360-2. ISSN 0022-2836. PMID 2231712.
- ↑ Gupta, Sudheer; Kapoor, Pallavi; Chaudhary, Kumardeep; Gautam, Ankur; Kumar, Rahul; Consortium, Open Source Drug Discovery; Raghava, Gajendra P. S. (13 September 2013). "In Silico Approach for Predicting Toxicity of Peptides and Proteins". PLOS ONE. 8 (9): e73957. Bibcode:2013PLoSO...873957G. doi:10.1371/journal.pone.0073957. ISSN 1932-6203. PMC 3772798. PMID 24058508.
- ↑ Saha, S.; Raghava, G. P. S. (1 July 2006). "AlgPred: prediction of allergenic proteins and mapping of IgE epitopes". Nucleic Acids Research. 34 (Web Server): W202–W209. doi:10.1093/nar/gkl343. ISSN 0305-1048. PMC 1538830. PMID 16844994.
- ↑ Dimitrov, Ivan; Flower, Darren R.; Doytchinova, Irini (17 April 2013). "AllerTOP - a server for in silico prediction of allergens". BMC Bioinformatics. 14 (6): S4. doi:10.1186/1471-2105-14-S6-S4. ISSN 1471-2105. PMC 3633022. PMID 23735058.
- ↑ Doytchinova, Irini A.; Flower, Darren R. (5 January 2007). "VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines". BMC Bioinformatics. 8 (1): 4. doi:10.1186/1471-2105-8-4. ISSN 1471-2105. PMC 1780059. PMID 17207271.
- ↑ Vita, Randi; Blazeska, Nina; Marrama, Daniel; IEDB Curation Team Members; Shackelford, Deborah; Zalman, Leora; Foos, Gabriele; Zarebski, Laura; Chan, Kenneth; Reardon, Brian; Fitzpatrick, Sidne; Busse, Matthew; Coleman, Sara; Sedwick, Caitlin; Edwards, Lindy (6 January 2025). "The Immune Epitope Database (IEDB): 2024 update". Nucleic Acids Research. 53 (D1): D436–D443. doi:10.1093/nar/gkae1092. ISSN 0305-1048. PMC 11701597 Check
|pmc=value (help). PMID 39558162 Check|pmid=value (help). - ↑ Walker, John M., ed. (2005). The Proteomics Protocols Handbook. doi:10.1385/1592598900. ISBN 978-1-58829-343-5. Search this book on
- ↑ Jones, David T (17 September 1999). "Protein secondary structure prediction based on position-specific scoring matrices1". Journal of Molecular Biology. 292 (2): 195–202. doi:10.1006/jmbi.1999.3091. ISSN 0022-2836. PMID 10493868.
- ↑ Drozdetskiy, Alexey; Cole, Christian; Procter, James; Barton, Geoffrey J. (1 July 2015). "JPred4: a protein secondary structure prediction server". Nucleic Acids Research. 43 (W1): W389–W394. doi:10.1093/nar/gkv332. ISSN 0305-1048. PMC 4489285. PMID 25883141.
- ↑ Sen, T. Z.; Jernigan, R. L.; Garnier, J.; Kloczkowski, A. (1 June 2005). "GOR V server for protein secondary structure prediction". Bioinformatics. 21 (11): 2787–2788. doi:10.1093/bioinformatics/bti408. ISSN 1367-4803. PMC 2553678. PMID 15797907.
- ↑ Jumper, John; Evans, Richard; Pritzel, Alexander; Green, Tim; Figurnov, Michael; Ronneberger, Olaf; Tunyasuvunakool, Kathryn; Bates, Russ; Žídek, Augustin; Potapenko, Anna; Bridgland, Alex; Meyer, Clemens; Kohl, Simon A. A.; Ballard, Andrew J.; Cowie, Andrew (August 2021). "Highly accurate protein structure prediction with AlphaFold". Nature. 596 (7873): 583–589. Bibcode:2021Natur.596..583J. doi:10.1038/s41586-021-03819-2. ISSN 1476-4687. PMC 8371605 Check
|pmc=value (help). PMID 34265844 Check|pmid=value (help). - ↑ Waterhouse, Andrew; Bertoni, Martino; Bienert, Stefan; Studer, Gabriel; Tauriello, Gerardo; Gumienny, Rafal; Heer, Florian T; de Beer, Tjaart A P; Rempfer, Christine; Bordoli, Lorenza; Lepore, Rosalba; Schwede, Torsten (2 July 2018). "SWISS-MODEL: homology modelling of protein structures and complexes". Nucleic Acids Research. 46 (W1): W296–W303. doi:10.1093/nar/gky427. ISSN 0305-1048. PMC 6030848. PMID 29788355.
- ↑ Zheng, Wei; Wuyun, Qiqige; Li, Yang; Liu, Quancheng; Zhou, Xiaogen; Peng, Chunxiang; Zhu, Yiheng; Freddolino, Lydia; Zhang, Yang (23 May 2025). "Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER". Nature Biotechnology: 1–13. doi:10.1038/s41587-025-02654-4. ISSN 1546-1696. PMID 40410405 Check
|pmid=value (help). - ↑ Colovos, Chris; Yeates, Todd O. (September 1993). "Verification of protein structures: Patterns of nonbonded atomic interactions". Protein Science. 2 (9): 1511–1519. doi:10.1002/pro.5560020916. ISSN 0961-8368. PMC 2142462. PMID 8401235.
- ↑ Laskowski, R. A. (1 January 2009). "PDBsum new things". Nucleic Acids Research. 37 (Database): D355–D359. doi:10.1093/nar/gkn860. ISSN 0305-1048. PMC 2686501. PMID 18996896.
- ↑ Bugnon, Marine; Röhrig, Ute F; Goullieux, Mathilde; Perez, Marta A S; Daina, Antoine; Michielin, Olivier; Zoete, Vincent (5 July 2024). "SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina". Nucleic Acids Research. 52 (W1): W324–W332. doi:10.1093/nar/gkae300. ISSN 0305-1048. PMC 11223881 Check
|pmc=value (help). PMID 38686803 Check|pmid=value (help). - ↑ Ashizawa, Ryota; Kotelnikov, Sergei; Khan, Omeir; Li, Stan Xiaogang; Glukhov, Ernest; Cao, Xin; Lazou, Maria; Bekar-Cesaretli, Ayse; Hailegeorgis, Derara; Averkava, Veranika; Zhu, Yimin; Jones, George; Yu, Hao; Kalitin, Dmytro; Stepanenko, Darya (January 2026). "Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16". Proteins: Structure, Function, and Bioinformatics. 94 (1): 183–191. doi:10.1002/prot.70066. ISSN 0887-3585. PMC 12750026 Check
|pmc=value (help). PMID 41115690 Check|pmid=value (help). - ↑ Goodsell, David S.; Sanner, Michel F.; Olson, Arthur J.; Forli, Stefano (January 2021). "The AutoDock suite at 30". Protein Science. 30 (1): 31–43. doi:10.1002/pro.3934. ISSN 0961-8368. PMC 7737764 Check
|pmc=value (help). PMID 32808340 Check|pmid=value (help). - ↑ Abraham, Mark James; Murtola, Teemu; Schulz, Roland; Páll, Szilárd; Smith, Jeremy C.; Hess, Berk; Lindahl, Erik (1 September 2015). "GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers". SoftwareX. 1–2: 19–25. Bibcode:2015SoftX...1...19A. doi:10.1016/j.softx.2015.06.001. ISSN 2352-7110.
- ↑ López-Blanco, José Ramón; Aliaga, José I.; Quintana-Ortí, Enrique S.; Chacón, Pablo (1 July 2014). "iMODS: internal coordinates normal mode analysis server". Nucleic Acids Research. 42 (W1): W271–W276. doi:10.1093/nar/gku339. ISSN 1362-4962. PMC 4086069. PMID 24771341.
- ↑ Huang, Xin; Chen, Rong; Sun, Meiling; Peng, Yan; Pu, Qinlin; Yuan, Yi; Chen, Gangyi; Dong, Juan; Du, Feng; Cui, Xin; Tang, Zhuo (7 May 2020). "Frame-shifted proteins of a given gene retain the same function". Nucleic Acids Research. 48 (8): 4396–4404. doi:10.1093/nar/gkaa169. ISSN 0305-1048. PMC 7192591 Check
|pmc=value (help). PMID 32187359 Check|pmid=value (help). - ↑ Hoff, Katharina J. (12 November 2009). "The effect of sequencing errors on metagenomic gene prediction". BMC Genomics. 10 (1): 520. Bibcode:2009BMCG...10..520H. doi:10.1186/1471-2164-10-520. ISSN 1471-2164. PMC 2781827. PMID 19909532.
- ↑ Goodswen, Stephen J.; Kennedy, Paul J.; Ellis, John T. (1 October 2017). "On the application of reverse vaccinology to parasitic diseases: a perspective on feature selection and ranking of vaccine candidates". International Journal for Parasitology. ApiCOWplexa 2017 – 4th International Meeting on Apicomplexan Parasites in Farm Animals. 47 (12): 779–790. doi:10.1016/j.ijpara.2017.08.004. ISSN 0020-7519. PMID 28893639.
- ↑ Zumárraga, Javier; López, Daniel; Sotillo, Javier; McConnell, Michael J.; Martín-Galiano, Antonio J. (5 February 2026). "Is the reverse vaccinology idea becoming exhausted?". Frontiers in Immunology. 17. doi:10.3389/fimmu.2026.1730217. ISSN 1664-3224. PMC 12916688 Check
|pmc=value (help). Unknown parameter|article-number=ignored (help)
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