Reliable B cell epitope predictions: impacts of method development and improved benchmarking

Cited by (678)

Items 601–678 of 678

1. Development of multi-epitope chimeric antigens for scrub typhus diagnostics and vaccines: An in-silico investigation
   Nima Dondu Namsa, Anutee Dolley, Himanshu Ballav Goswami, Dikshita Dowerah, Upalabdha Dey, Aditya Arun Kumar, Debashree Saikia Sharma, Vanlal Hmuaka, Rupak Mukhopadhyay, Debasree Kundu et al. · 2022 · Research Square
2. Fluorescent Imaging of Extracellular Fungal Enzymes Bound onto Plant Cell Walls
   Neus Gacias Amengual, Lena Wohlschlager, Florian Csarman, Roland Ludwig · 2022 · International Journal of Molecular Sciences
3. Peer Review #1 of "Enhancement of conformational B-cell epitope prediction using CluSMOTE (v0.1)"
   2020 · PeerJ Computer Science
4. Peer Review #3 of "Enhancement of conformational B-cell epitope prediction using CluSMOTE (v0.3)"
   2020 · PeerJ Computer Science
5. Peer Review #2 of "Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2, the etiologic agent of COVID-19 pandemic: an in silico approach (v0.1)"
   2020 · PeerJ
6. Peer Review #1 of "Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2, the etiologic agent of COVID-19 pandemic: an in silico approach (v0.1)"
   2020 · PeerJ
7. Peer Review #3 of "Enhancement of conformational B-cell epitope prediction using CluSMOTE (v0.1)"
   2020 · PeerJ Computer Science
8. Peer Review #3 of "Enhancement of conformational B-cell epitope prediction using CluSMOTE (v0.2)"
   2020 · PeerJ Computer Science
9. Pre-existing immunity to influenza viruses through infection and/or vaccination leads to viral mutational signatures associated with unique immune responses during a subsequent infection
   Melissa L. Rioux, Anni Ge, Anthony Yourkowski, Magen Ellen Francis, Mara McNeil, Alaa Selim, Bei Xue, Joseph Darbellay, Alyson A. Kelvin · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
10. Identification of Immunogenic T and B-Cell Epitope Peptides of Rubella Virus E1 Glycoprotein towards the Development of Highly Specific Immunoassays and Vaccine
    Prashanth Rajendiran, Nithiyanandan Saravanan, Mageshbabu Ramamurthy, Rajasekar Aruliah, Balaji Nandagopal · 2022 · Journal of Advances in Biology & Biotechnology
11. Construction of Multi-Epitopes Vaccine Candidate against SARS-CoV-2 D614G Variant
    Siti Asmaa Mat Jusoh, Danesh Thangeswaran, Muhammad Syahir Hakimi Mohd Hazli, Mohd Firdaus‐Raih, Nurulasma Abdullah, Shaharum Shamsuddin · 2022 · Sains Malaysiana
12. Optimisation of immunocytochemistry methodology for the detection of endogenous eIF2B localised foci
    Madalena I. Ribeiro de Oliveira, Filipe M. Hanson, Rachel E. Hodgson, Alison K. Cross, Susan G. Campbell, K. Elizabeth Allen · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
13. Developing a Next-generation Multitudinous Epitope-based Vaccine Against Biotinidase Deficiency; An Immunoinformatics-based Approach
    M. Anitha, Radha Mahendran · 2022 · Journal of Pharmaceutical Negative Results
14. Reducing the Immunogenicity of Pulchellin A-Chain, Ribosome-Inactivating Protein Type 2, by Computational Protein Engineering for Potential New Immunotoxins
    Reza Maleki, Libing Fu, Ricardo Sobhie Diaz, Francisco Eduardo Gontijo Guimarães, Otávio Cabral-Marques, Gustavo Cabral‐Miranda, Mohammad Sadraeian · 2023 · J — Multidisciplinary Scientific Journal
15. Characterization of immunomodulatory B-cells and T-cells to generate extremely targeted immunoassays and vaccines
    Main Bashir Ahmad, Fatima Rezayee, Muhammad Fayaz Khan, Muhammad Hassan, Muhammad Naveed, Mehboob Alam · 2023 · International Journal of Health Sciences
16. Dynamic structural analysis-based epitope prediction of Exendin-4 in aqueous solution
    Jianfeng He, Jing Li, Kingsley Leung · 2023 · Physical review. E
17. Immunoinformatics design of B-cell multi-epitope peptide for the diagnosis of Methicillin Resistant Staphylococcus aureus (MRSA) infection
    Simeon Kayowa Olatunde, Joshua B. Owolabi, Bolaji Oluwabusayo Ayinde, Shauna Angella Ebanks, Edla Sophia Vidale, Elijah Kolawole Oladipo, Yakubu Adekunle Alli, Enoch Oluwalonimi Adewara · 2023 · F1000Research
18. Development of attenuated coxsackievirus B3 vectored intranasal pre-emptive pan-coronavirus vaccine
    Huixiong Deng, Xuanting He, Yanlei Li, Haoyang Wang, Shenmiao Wang, Liming Gu, Hengyao Zhang, Jiacheng Zhu, Rui Li, Gefei Wang · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
19. Identifikation und Analyse von Interaktionen Erreger-spezifischer Antikörper mit Proteinen des fötalen Gehirns
    Aaron David Kleine · 2023
20. The role of eIF2Bα in the integrity of eIF2B bodies
    Madalena I. Ribeiro de Oliveira · 2023 · Sheffield Hallam University
21. Peptide Engineering Approach to Introduce an Improved Calcitonin Mutant
    Mahboubeh Zarei, B. Abedini, Ali Dehshahri, Manica Negahdaripour · 2024 · Molecular Biology
22. Designing a Novel Multi-epitope Peptide as a Potential Serodiagnosis Marker for the Diagnosis of Acinetobacter baumannii: An In silico Approach
    Maryam Rezaee, Mohsen Mohammadi, Amir Savardashtaki, Mohammad Reza Rahbar, Navid Nezafat · 2024 · Current Proteomics
23. Vaccinomics
    Madhulika Jha, Nidhi Yadav, Swasti Rawal, Payal Gupta, Navin Kumar, Ravi Kumar Yadav, Tara Chand Yadav · 2024 · Elsevier eBooks
24. Expression of Recombinant Stonustoxin Alpha Subunit and Preparation of polyclonal antiserum for Stonustoxin Neutralization Studies
    Amir Sajjad Hojjati Razgi, Shahram Nazarian, Hossein Samiei-Abianeh, Amir Vazirizadeh, Emad Kordbacheh, Seyed Mojtaba Aghaie · 2024 · The Protein Journal
25. Differential epitope prediction across diverse circulating variants of SARS-COV-2 in Brazil
    Vanessa de Melo Cavalcanti-Dantas, Brenda Fernandes, Pedro Henrique Lopes Ferreira Dantas, Glaucielle Ramalho Uchoa, Andrei Félix Mendes, Waldecir Oliveira de Araújo Júnior, Lúcio Roberto Cançado Castellano, Ana Isabel Vieira Fernandes, Luíz Ricardo Goulart, Renato Antônio dos Santos Oliveira et al. · 2024 · Computational Biology and Chemistry
26. Exploiting the Role of Features for Antigens-Antibodies Interaction Site Prediction
    Michela Quadrini, Carlo Ferrari · 2024 · Methods in molecular biology
27. Immunogenicity study of a Novel DNA-Based HCV vaccine candidate
    Yasmine S. El Abd · 2024 · Egyptian journal of Immunology
28. Predicting immune response targets in orthoflaviviruses through sequence homology and computational analysis
    Varshini Are, Rajarshi Roy, Sandeep Kumar Dhanda, Sanchit Neema, Neha Sahu, Nitin Adithya, Ritudhwaj Tiwari, Parimal Kar, Debasis Nayak · 2024 · Journal of Molecular Modeling
29. Profiling of linear B-cell epitopes against human coronaviruses in pooled sera sampled early in the COVID-19 pandemic
    Emil Bach, Mustafa Ghanizada, Nikolaj Kirkby, Søren Buus, Thomas Østerbye · 2024 · Open Research Europe
30. Exploring B-cell epitope conservation and antigenicity shift in current COVID-19 variants: Analyzing spike-antibody interactions for therapeutic uses
    Alankar Roy, Ishani Paul, T. Manna Paul, Aritrika Dihidar, Sujay Ray · 2024 · Biochemical and Biophysical Research Communications
31. Beyond prevention: in silico designing a one-two punch novel therapeutic vaccine candidate against major oncoproteins of HPV 16, 18, 31, and 45 and subsequent cervical cancer
    Hadi Esmaeili Gouvarchin Ghaleh, Behzad Shahbazi, Mohammad Hossein Ataee, Mahdieh Farzanehpour, Ali Najafi · 2024 · Molecular Simulation
32. Mapeamento de epitopos para células B de bovinos em antígenos de carrapatos: uma análise comparativa entre métodos in silico e in vitro
    Luiz Gustavo Nogueira de Almeida · 2019 · Digital Library of Theses and Dissertations (Universidade de São Paulo)
33. Moringa oleifera Lam. leaves-induced food allergic responses by modulating the Th1/Th2 immune balance in a multi-functional mode
    Shuang Song, Xi Chuyu, Su Hairan, Liu Xiaoxue, Hao Yang, Wenjie Li, Jing Xie, Liang Tao, Shijun Li, Jun Sheng et al. · 2025 · Food Science and Human Wellness
34. Epitope Predictions
    Roman Kogay, Christian Schönbach · 2019 · Elsevier eBooks
35. Determination of Immunotherapeutic Epitopes of Human Papillomavirus Type 16 by Bioinformatics Approaches
    Betül Akçeşme, Raneem Aldadah, Aiša Galijatović, Maida Hajdarpašić · 2025 · Lecture notes in networks and systems
36. Epi4Ab: a data-driven prediction model of conformational epitopes for specific antibody VH/VL families and CDRs sequences
    Tran, Nhan Dinh, Subramani, Krithika, Su, Chinh Tran-To · 2025 · mAbs
37. Immunoinformatics Design and Identification of B-Cell Epitopes from Vespa affinis PLA1 Allergen
    Sophida Sukprasert, Siriporn Nonkhwao, Thitijchaya Thanwiset, Walter Keller, Sakda Daduang · 2025 · Toxins
38. An improved deep learning model for immunogenic B epitope prediction
    Rakshanda Sajeed, Swatantra Pradhan, Rajgopal Srinivasan, Sadhna Rana · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
39. Computational Design of Soluble CCR8 Analogues with Preserved Antibody Binding
    Trang Nguyen, Songming Liu, Yifan Li, Longfei Cong, Roger Shek, Tek Hyung Lee, Yi Li, Per Jr Greisen · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
40. Structure-based Predictions of Conformational B Cell Epitopes by Protein Language Model and Deep Learning
    Yuhao Zhang, Zhaoqian Su, Felipe Vilicich, Xiaohan Kuang, Yunchao Liu, Grace Zhang, Yinghao Wu · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
41. HyperBind2: Multi-Shot Learning Enables Progressive Improvement in Computational Antibody Discovery
    Daniel Dell'uomo, Andrew Satz, Brett Averso · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
42. Additional file 1 of In silico designing of a novel epitope-based candidate vaccine against Streptococcus pneumoniae with introduction of a new domain of PepO as adjuvant
    Zohreh Bahadori, Mona Shafaghi, Hamid Madanchi, Ranjbar, Mohammad Mehdi, Shabani, Ali Akbar, Seyed Fazlollah Mousavi · 2022 · Figshare
43. Additional file 1 of Identification and genetic characterization of a minor norovirus genotype, GIX.1[GII.P15], from China
    Chen, Yanli, Qiongwen Wu, Guiman Li, Li, Hongzhe, Li, Wenlong, Heng Li, Qin, Li, Zheng, Huiwen, Liu, Changkun, Hou, Min et al. · 2022 · Figshare
44. Additional file 2 of Identification and genetic characterization of a minor norovirus genotype, GIX.1[GII.P15], from China
    Chen, Yanli, Qiongwen Wu, Guiman Li, Li, Hongzhe, Li, Wenlong, Heng Li, Qin, Li, Zheng, Huiwen, Liu, Changkun, Hou, Min et al. · 2022 · Figshare
45. Deep learning for B-cell epitope prediction and receptor–antigen binding prediction
    Feng Jiang, Junzhou Huang · 2025 · Elsevier eBooks
46. Informatics in allergology
    Mansi Pandit, N. Latha · 2025 · Allergy medicine.
47. QGraphTad: A Novel Quantum-Inspired Method for Conformational B-Cell Epitope Prediction
    Buzhong Zhang, Zhaolun Yao, Yajun Xu, Lijun Quan · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
48. Comparative Binding Dynamics of Minibinder 8.6 and HBD3 With TLR3 as Adjuvants for Developing a Peptide‐Based Multi‐Epitope Subunit Vaccine Against mCRPC : A Molecular Dynamics Study
    Ishani Paul, Soumyadeep Ray, Muskan Tewari, Mowmita Saha, Sujay Ray · 2026 · Proteins Structure Function and Bioinformatics
49. Computational engineering of Amphibalanus amphitrite CP19k cement protein to design reduced immunogenicity underwater bioadhesive
    Gelareh Zargari, Maryam Azimzadeh Irani, Mohammad Assadizadeh, Sheida Khoniki, Mohammad Javad Eslami · 2026 · Results in Chemistry
50. Computational prediction and molecular simulation-based development of a multi-epitope mRNA vaccine targeting capsule polysaccharide proteins of Enterobacter cloacae
    Shubhi Singh, Priya Swaminathan · 2026 · Computational Biology and Chemistry
51. In-silico Molecular Investigation of Caulobacter Crescentus Bioadhesive Proteins
    Yeganeh Kayalha, Maryam Azimzadeh Irani · 2025 · National and International Iranian Conference on Biomedical Engineering (ICBME)
52. Multi-tope subunit vaccine for human anthrax through pan-genome-based reverse vaccinology approach
    Raison Joseph, Subalakshmi Kaarmegam Pandiarajan, Jeyaprakash Rajendhran · 2026 · Molecular Genetics and Genomics
53. Etude de la variole ovine en Tunisie et caractérisation des protéines virales impliquées dans la réponse immunitaire anti-capripoxvirus
    Faten Ben Chehida · 2017 · theses.fr (ABES)
54. A docking-based method for in silico epitope determination
    Shifa Tahir · 2018 · theses.fr (ABES)
55. Mathematical foundations of antibody affinity maturation
    Irène Balelli · 2016 · theses.fr (ABES)
56. An integrated computational antigen discovery pipeline with hierarchical filtering for emerging viral variants
    Raj S. Roy, Jaemin Oh, A N M Nafiz Abeer, María I. Giraldo, Tesuro Ikegami, Scott C. Weaver, Nikolaos Vasilakis, Byung-Jun Yoon, Xiaoning Qian · 2026 · NAR Molecular Medicine
57. HAIRpred2: Human Host-Specific Prediction of Antibody-Interacting Residues Using Hybrid Physicochemical and Structural Features
    Naman Kumar Mehta, Ruchir Sahni, Nishant Kumar, Gajendra P. S. Raghava · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
58. Pressure–cooling remodeling of TMV coat protein reveals mechanically partitioned capsid dynamics and selective epitope masking
    Carlos Francisco Sampaio Bonafé, Juan Philippe Teixeira, Caio César de Melo Freire, Miklos Maximiliano Bajay, Daniel F de Lima Neto · 2026 · Research Square
59. Design of a multi-epitope Staphylococcus aureus vaccine integrating a protein A variant, α-hemolysin, and fibronectin-binding protein A through reverse vaccinology
    Hannia Michelle Prieto-Nevárez, Alejandro Tarango-García, Arturo Gutierrez‐Guerrero, Aristóteles Álvarez-Cardona, Saúl Oswaldo Lugo Reyes · 2026 · Scientific Reports
60. Immunologically Optimized Zmp1 Peptides Reveal a Translational Serological Biomarker Platform for Tuberculosis Diagnosis Across Disease Manifestations
    Omkar Shriram Zade, Sriram Yandrapally, Keerthana Choudari, Akshay Vaijinath Gaikwad, Rajanikant Panda, Venkata Sanjeev Kumar Neela, Kamakshi Prudhula Devalraju, V. V. Ramprasad Eedara, Mohammad Soheb Ansari, Chitra Chandrashekhar et al. · 2026 · medRxiv
61. HLA Binding Peptide-Based Designing of Non-Spike Universal Nanovaccine Against SARS-CoV-2: A Computational Approach
    Puja Jaishwal, Satarudra Prakash Singh · 2026 · Biophysica
62. Computational and Experimental Development of a Novel Multi‐Epitope Vaccine Candidate Against Bovine Leukaemia Virus
    Yasaman Dini, Tohid Piri Gharaghie, Elahe Hamdi, Pegah Goodarzi, Ronak Ahmadi · 2026 · Veterinary Medicine and Science
63. Systems-level design of a multi-epitope immunotherapeutic vaccine targeting EBV-associated oncogenesis
    Ssemuyiga Charles, Naddamba Assumpta · 2026 · Scientific Reports
64. The critical role of artificial intelligence and bioinformatics in accelerating peptide-based vaccine discovery for tackling global infectious diseases
    Nomathamsanqa Tholo, Gavin Markey, Ruairidh Harrigan, Preeti Pandey, Bodhayan Prasad, Ram Shankar Barai, David S. Gibson, Priyank Shukla · 2026 · Briefings in Bioinformatics
65. Self-amplifying mRNA vaccine cocktail against Staphylococcus aureus: A multi-epitope immunoinformatics and structural simulation framework
    Aysan Salemi, Mohammad Mostafa Pourseif, Behzad Jafari, Jaleh Barar, Yadollah Omidi · 2026 · World Journal of Microbiology and Biotechnology
66. Lineage Diversification and Evolutionary Dynamics of the Hemagglutinin–Neuraminidase Gene in Mumps Virus Genotype G
    Fuminori Mizukoshi, Miu Takada, Ryusuke Kimura, Wei Liu, Yasuyoshi Hatayama, Mayuko Nishi, Yuka Sato‐Fujimoto, Akira Kimura, Fumihiro Kato, Kei Miyakawa et al. · 2026 · Microorganisms
67. Machine Learning Applications in Vaccine Design
    Preena S. Parvathy, V. Anil Kumar, Raja Biswas, C. Gopi Mohan · 2026 · Royal Society of Chemistry eBooks
68. Pocket restraints guided by B‐cell epitope prediction improve Chai‐1 antibody–antigen structure modeling
    Joakim Nøddeskov Clifford, Morten Nielsen · 2026 · Protein Science
69. Molecular characterization of a rare norovirus GII.8[P8] strain detected during pediatric acute gastroenteritis surveillance in Harbin, China
    Yuan Tian, Xiqiao Du, Tuo Dong, Zhe Zhang · 2026 · Virus Genes
70. Computational Design of a Therapeutic Self-Assembled Peptide Nanovaccine Against Breast Cancer
    Bahareh Vakili, Younes Ghasemi, Mohammad Hossein Morowvat, Navid Nezafat, Manica Negahdaripour · 2026 · Journal of Cluster Science
71. GCAT-BCE: A hybrid GCN-GAT framework for enhanced conformational B-cell epitope prediction
    Rui Liu, Yuanyuan Lei, Wentao Xu, Hanxi Yu, Ting Long, Mei Ying Hu · 2026 · Computational Biology and Chemistry
72. 花粉食物アレルギー症候群の原因となるGRPファミリーアレルゲンPru p 7およびCry j 7の構造および安定性の解析
    靖康 鄭 · 2025 · Institutional Repositories DataBase (IRDB)
73. In silico design of a novel peptide-based vaccine candidate against Streptococcus pneumoniae
    jahangir sabzevari, Mona Shafaghi, Zohreh Bahadori, Zahra Nabizadeh · 2026 · In Silico Pharmacology
74. Novel L-Asparaginases from the human gut microbiome: Genome mining, biochemical characterization, and in vitro anti-leukemic activity
    Duygu Delican, Ozan Kılıçkaya, Özkan Özden, Yunus Ensari · 2026 · Bioorganic Chemistry
75. Computational design and translational development of TCR-mimic scFv antibodies for peptide-HLA neoantigen targeting
    Sarfaraz K. Niazi, Matthias Magoola, Zamara Mariam · 2026 · npj Drug Discovery.
76. Epitope-guided optimization improves the protective efficacy of NA-based mRNA vaccines against seasonal influenza A(H3N2) virus
    Hyunbeen Kim, Sangyi Lee, Seunghye Cho, Woojin Shin, Soyoung Lee, Atanas Vladimirov Demirev, Taeyoung Lee, You-Jin Kim, Dokeun Kim, Sae Am Song et al. · 2026 · The Journal of Microbiology
77. In silico mapping of Leptospira interrogans putative carboxypeptidases: functional domains, predicted virulence signatures, and epitope identification for potential subunit vaccine candidates
    Julia E. L. Paixao, Felipe L. Santos, Igor R. M. Silva, Bruno B. Foltran, João P. Gaspar, Henrique Machado Pires, Ana Barbara Nunes, Lara Scaranello Verdi, Mayara H. Stancey, Ana L. T. O. Nascimento et al. · 2026 · Frontiers in Bioinformatics
78. Applying Stacked and Cascade Generalizations to B-cell Epitope Prediction
    Yuh‐Jyh Hu, Shun-Chien Lin, Yu‐Lung Lin · 2014