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Epitope mapping

Epitope mapping is the process of identifying and characterizing the specific regions, known as epitopes, on an antigen's surface that are recognized and bound by antibodies or other immune molecules, such as T-cell receptors.^[1] These epitopes can be linear, consisting of contiguous amino acid sequences, or conformational, involving spatially proximate residues from non-adjacent parts of the protein structure, and mapping them elucidates the molecular basis of immune recognition.^[2] The technique is fundamental in immunology and biotechnology, enabling the design of epitope-based vaccines that target immunogenic sites to elicit protective antibody responses against pathogens, as demonstrated in efforts against viruses like SARS-CoV-2.^[2] By revealing antibody-antigen binding interfaces, epitope mapping informs the development of therapeutic monoclonal antibodies with enhanced specificity and reduced off-target effects, while also aiding in the prediction of immune escape variants through mutational analysis.^[3] Its applications extend to diagnostics, where mapped epitopes serve as biomarkers, and to protein engineering for more effective biologics.^[1] A range of experimental and computational methods underpin epitope mapping, with X-ray crystallography serving as the gold standard for providing atomic-resolution structures of antigen-antibody complexes, though it is often limited by crystallization challenges.^[2] Complementary approaches include cryo-electron microscopy for visualizing large complexes, deep mutational scanning to assess binding impacts of amino acid substitutions, and peptide array assays for screening linear epitopes across antigen sequences.^[3] Recent advances incorporate machine learning algorithms to predict epitopes from sequence data, accelerating discovery in vaccine and therapeutic design.^[4]

Fundamentals

Definition and Overview

Epitope mapping is the process of identifying the specific regions, known as epitopes or antigenic determinants, on an antigen that are recognized and bound by antibodies, T-cell receptors, or other components of the immune system.^[5] Antigens are molecules, often proteins, that can elicit an immune response by being perceived as foreign by the host organism. Epitopes represent the minimal structural features of these antigens responsible for such recognition; linear epitopes consist of continuous sequences of typically 5-17 amino acids, while conformational epitopes involve spatially proximate residues that form a three-dimensional structure critical for binding.^[6] This mapping elucidates the molecular basis of antigen-antibody interactions, which is fundamental to understanding adaptive immunity.^[5] The origins of epitope mapping trace back to the 1980s, emerging from foundational studies in antigen-antibody interactions during the early era of monoclonal antibody development.^[7] A seminal advancement came in 1984 with the introduction of peptide synthesis techniques by H. Mario Geysen and colleagues, who developed a method to systematically probe viral antigens using overlapping synthetic peptides, achieving resolution down to a single amino acid. This approach marked a shift from rudimentary serological assays to more precise serological and biochemical strategies, laying the groundwork for high-resolution epitope identification that has since evolved with advances in molecular biology.^[7] In general, the epitope mapping process begins with the selection of a target antigen and the immune component of interest, such as a specific antibody, followed by systematic analysis to pinpoint binding sites through comparison of reactivity patterns across antigen variants.^[2] This workflow culminates in the characterization of epitope location and structure, providing insights into immune recognition mechanisms.^[5] Epitope mapping serves dual purposes: in research, it advances fundamental knowledge of immunological specificity, whereas in applied contexts like drug development, it guides the engineering of therapeutics that selectively target protective or neutralizing epitopes.^[2]

Types of Epitopes

Epitopes are broadly classified into B-cell and T-cell epitopes based on the immune cells they interact with and their structural properties. B-cell epitopes are recognized directly by B-cell receptors or antibodies on the surface of native antigens, while T-cell epitopes are presented as peptide fragments by major histocompatibility complex (MHC) molecules to T cells.^[8]^[9] B-cell epitopes are surface-exposed regions of antigens and are divided into linear and conformational types. Linear B-cell epitopes consist of continuous sequences of typically 5-17 amino acid residues that are sequentially contiguous in the primary protein structure.^[10]^[11] In contrast, conformational or discontinuous B-cell epitopes involve amino acids that are distant in the primary sequence but brought into close proximity by the three-dimensional folding of the protein, often forming complex structures dependent on the native antigen conformation.^[8]^[12] Approximately 90% of B-cell epitopes are conformational, highlighting their prevalence in natural immune responses to folded proteins.^[13] Examples of linear B-cell epitopes include segments in the V3 loop of HIV-1 gp120, which are recognized by neutralizing antibodies and contribute to viral entry inhibition.^[14] Conformational B-cell epitopes are exemplified by those in the head domain of influenza hemagglutinin, where discontinuous residues form the receptor-binding site targeted by broadly neutralizing antibodies across subtypes.^[15]^[16] T-cell epitopes, unlike B-cell epitopes, are not directly accessible on the antigen surface but arise from intracellular processing of proteins into short peptide fragments. These peptides, typically 8-11 amino acids long for MHC class I presentation (recognized by CD8+ T cells), are generated via proteasomal degradation in the cytosol followed by transport to the endoplasmic reticulum for loading onto MHC class I molecules.^[9]^[17] For MHC class II presentation (recognized by CD4+ T cells), peptides are longer, ranging from 13-25 amino acids, and result from endosomal/lysosomal degradation of exogenous antigens.^[9]^[18] T-cell epitopes must possess specific MHC-binding motifs, such as anchor residues at positions 2 and 9 for HLA-A*02:01 alleles, where leucine is often preferred at position 2 and valine or leucine at the C-terminus to fit into MHC pockets.^[19]^[20] Key differences between B-cell and T-cell epitopes influence their recognition and mapping. B-cell epitopes are generally larger and solvent-accessible on the antigen exterior, enabling direct antibody binding without processing, whereas T-cell epitopes are inherently linear after proteolytic cleavage and require MHC restriction, with binding affinity dictated by anchor residues and processing pathways.^[8]^[9] These distinctions are critical for strategies in vaccine design, where conformational B-cell epitopes may elicit humoral responses and T-cell epitopes promote cellular immunity.^[13]

Importance and Applications

Antibody and Therapeutic Development

Epitope mapping plays a crucial role in elucidating the mechanism of action for therapeutic monoclonal antibodies (mAbs) by distinguishing blocking epitopes, which interfere with ligand-receptor interactions, from non-blocking ones that may enhance effector functions without direct inhibition. For instance, in cancer immunotherapies, mapping PD-1 inhibitors like nivolumab and pembrolizumab reveals epitopes on the PD-1 IgV domain, particularly the FG and BC loops, that block PD-1/PD-L1 binding to restore T-cell activity. This differentiation aids in optimizing antibodies for specific therapeutic outcomes, such as immune checkpoint blockade, where precise epitope localization ensures efficacy against tumor evasion mechanisms.^[21]^[22] In the characterization process for antibody therapeutics, epitope mapping confirms specificity, affinity, and cross-reactivity, which are essential for regulatory approval, particularly for biosimilars. By identifying the exact binding sites, developers can demonstrate similarity to reference products, assessing risks like immunogenicity from overlapping epitopes that might trigger anti-drug antibodies. For FDA approval of biosimilars, such as those targeting HER2, mapping ensures functional equivalence without unintended off-target effects, supporting comparability in higher-order structure and binding profiles. Quantitative metrics, including epitope density and accessibility, are evaluated using dissociation constants (KD), where high-affinity mAbs typically exhibit KD values in the low nanomolar range (e.g., 0.1-10 nM), indicating strong, therapeutically relevant interactions.^[23]^[24] A prominent case is trastuzumab (Herceptin), approved pre-2020 for HER2-positive breast cancer, where epitope mapping identified a conformational epitope in domain IV of HER2, avoiding overlap with regions linked to immunogenicity while enabling receptor dimerization inhibition. This mapping informed development by confirming the antibody's specificity to tumor-overexpressed HER2, minimizing cross-reactivity with related receptors like EGFR. In the development pipeline, epitope mapping integrates from hybridoma screening, where initial clones are selected for target binding, to epitope binning assays that group antibodies by competitive binding sites, facilitating cocktail therapies with non-overlapping epitopes for enhanced potency, as seen in multi-specific antibody designs.^[25]^[26]^[27]

Intellectual Property Protection

Epitope mapping serves as a critical tool in intellectual property protection for biologics, particularly monoclonal antibodies (mAbs), by delineating the precise binding sites on antigens that confer novelty and specificity to inventions. This process generates structural and functional data that supports patent claims, distinguishing new antibodies from prior art and satisfying legal requirements for disclosure. In the context of U.S. patent law, epitope mapping provides evidence required under 35 U.S.C. §112(a) for enablement and written description, ensuring that applicants demonstrate possession of the full scope of their claimed genus of antibodies without undue experimentation.^[28] For instance, high-resolution mapping at the amino acid level, such as through co-crystallography or mutagenesis, identifies unique epitopes that enable broader claims while avoiding rejections for insufficiency.^[28] A prominent case illustrating the interplay between epitope mapping and patent validity is the 2023 U.S. Supreme Court ruling in Amgen Inc. v. Sanofi, where broad functional claims to antibodies binding specific residues on the PCSK9 protein were invalidated for failing enablement under 35 U.S.C. §112(a).^[29] The Court emphasized that genus claims based solely on function—without structural details like epitope specificity—do not adequately enable the skilled artisan to make and use the invention across its scope, as the antibody field is highly unpredictable.^[29] Epitope mapping addresses this by providing structural claims that map overlapping or distinct binding sites, allowing patentees to differentiate competing antibodies in disputes; for example, post-ruling strategies incorporate paratope-epitope data to support narrower, yet robust, genus claims.^[30] Such mapping has been central to high-profile litigation, including earlier iterations of Amgen v. Sanofi and Biogen v. GlaxoSmithKline, where epitope differences established non-obviousness and infringement boundaries.^[28] In commercial strategies, biotech firms leverage epitope mapping to safeguard trade secrets alongside patents, particularly for conformational epitopes in mAb portfolios that are challenging to reverse-engineer without disclosure.^[31] By claiming antibodies specific to unique conformational epitopes, companies can protect proprietary variants while maintaining flexibility in development, as trade secret protection for antibodies is often limited by the need for eventual regulatory disclosure in therapeutics.^[31] This approach is especially valuable in portfolios targeting complex antigens, where mapping data enables claims to epitope-binding affinity or avidity, enhancing enforceability against biosimilars.^[31] Globally, requirements for epitope data in patent filings differ between the European Patent Office (EPO) and the U.S. Patent and Trademark Office (USPTO), influencing filing strategies. The EPO accepts broader epitope-based claims if supported by an inventive step, such as a technical effect tied to the epitope, and requires fewer representative examples, as seen in cases like T 1964/18 upholding functional epitope definitions.^[32] In contrast, the USPTO imposes stricter enablement and written description standards under 35 U.S.C. §112, demanding detailed structural data and multiple species to cover the claim scope, often rejecting epitope-alone claims post-Amgen v. Sanofi.^[33] These disparities lead applicants to tailor disclosures, providing more comprehensive mapping for U.S. filings while emphasizing inventive contributions in Europe.^[32] The economic impact of epitope mapping in IP protection is significant, as it bolsters patent grants in the biologics market—valued at approximately USD 486 billion as of 2025—and mitigates costly litigation by clarifying claim boundaries and reducing invalidation risks.^[34] In disputes over mAbs, which dominate biologics revenue, mapping data has proven essential in resolving infringement, potentially averting multimillion-dollar verdicts and accelerating market exclusivity worth billions for successful therapeutics.^[28]

Vaccine Design and Diagnostics

Epitope mapping plays a crucial role in vaccine design by identifying immunodominant epitopes on pathogen antigens, enabling the development of subunit vaccines that elicit targeted immune responses. For instance, in the human papillomavirus (HPV) vaccine, mapping of conformational epitopes on the L1 major capsid protein has guided the production of virus-like particles (VLPs) that mimic native virion structures, inducing neutralizing antibodies against high-risk HPV types. This approach has been instrumental in the formulation of prophylactic vaccines like Gardasil, which target these L1 epitopes to prevent cervical cancer.^[35] Reverse vaccinology integrates epitope mapping with genomic analysis to prioritize pathogen proteins for vaccine candidates, focusing on surface-exposed epitopes likely to induce protective immunity. By screening entire pathogen proteomes for B-cell and T-cell epitopes, this method accelerates antigen selection and has been applied to bacterial and viral pathogens, reducing reliance on traditional empirical approaches.^[36] Pre-2020 applications include epitope mapping of the Zaire ebolavirus glycoprotein (GP), where linear and conformational epitopes on the GP1 subunit were identified to inform vaccine constructs like the rVSV-ZEBOV vaccine, enhancing antibody-mediated neutralization during the 2014-2016 outbreak. Similarly, for Zika virus, mapping of epitopes on the envelope (E) protein, particularly the glycan loop in domain I, has supported subunit vaccine designs that elicit cross-reactive antibodies, addressing the virus's rapid global spread in 2015-2016.^[37]^[38] In diagnostics, epitope mapping facilitates the creation of serodiagnostic tools by pinpointing linear B-cell epitopes suitable for ELISA-based assays, which detect epitope-specific antibodies in patient sera for disease surveillance. For example, in Lyme disease, conserved epitopes from Borrelia burgdorferi outer surface protein C have been mapped and incorporated into peptide ELISAs, improving specificity and enabling early detection in endemic areas. These assays support public health monitoring by distinguishing active infections from past exposures.^[39] Multi-epitope vaccine strategies leverage epitope mapping to combine T-cell and B-cell epitopes into polyvalent constructs, broadening immune coverage and enhancing vaccine durability against antigenic variants. By linking cytotoxic T-lymphocyte (CTL), helper T-cell (HTL), and B-cell epitopes from conserved pathogen regions, these designs promote both humoral and cellular responses, as demonstrated in computational models for viral pathogens. Such approaches aim to overcome immune escape and improve efficacy in diverse populations.^[40] Epitope mapping contributes to public health by identifying conserved epitopes for outbreak response vaccines, such as universal influenza vaccines targeting the hemagglutinin stem region. Mapping these stable epitopes across influenza A subtypes has informed chimeric and mosaic vaccine platforms, potentially reducing seasonal flu burden and preparing for pandemics through cross-protective immunity.^[41]

Methods

Experimental Techniques

Experimental techniques for epitope mapping involve direct laboratory interrogation of antibody-antigen interactions to empirically identify binding sites, with methods selected based on desired resolution, throughput, and epitope complexity. These approaches generate data on epitope location, residue contributions, and structural features, often complementing each other for comprehensive characterization. High-resolution structural methods deliver atomic-level details of epitope-paratope interfaces. X-ray crystallography remains the gold standard, producing structures of antibody-antigen complexes at resolutions of 2-3 Å to reveal precise hydrogen bonds, van der Waals contacts, and other interactions.^[42] Cryo-electron microscopy (cryo-EM) complements this for larger or flexible complexes, such as viral spike proteins, achieving near-atomic resolutions, often 1.5-3 Å, following post-2010 advancements in direct electron detectors and image processing algorithms that enabled the "resolution revolution."^[43] Biochemical methods probe functional epitope contributions through targeted perturbations. Site-directed mutagenesis via alanine scanning systematically substitutes surface residues with alanine, measuring binding affinity changes—often as ΔΔG values exceeding 1 kcal/mol—to pinpoint energetically critical residues in both linear and conformational epitopes.^[44] Hydrogen-deuterium exchange mass spectrometry (HDX-MS) assesses epitope solvent exposure by tracking deuterium incorporation rates in amide hydrogens, where antibody binding induces protection (reduced exchange) in epitope regions, revealing dynamic conformational aspects at peptide-level resolution.^[45] High-throughput techniques accelerate mapping across entire antigens. Shotgun mutagenesis generates comprehensive libraries of single-residue variants of the antigen displayed on mammalian cell surfaces, using flow cytometry to detect binding disruptions and map conformational epitopes at amino acid resolution with >95% coverage.^[46] Peptide arrays, suited for linear epitopes, immobilize overlapping synthetic peptides (e.g., 15-mers offset by one residue) on a solid support, enabling parallel screening via antibody binding assays to localize sequential motifs.^[47] Display-based and cross-linking methods extend applicability to complex epitopes. Phage display presents randomized or fragmented antigen libraries on bacteriophage surfaces for iterative affinity selection and sequencing, identifying mimotopes that approximate native epitopes.^[48] Yeast surface display similarly expresses antigen variants on yeast cells, leveraging fluorescence-activated cell sorting (FACS) for quantitative affinity-based enrichment and epitope delineation.^[49] Cross-linking mass spectrometry (XL-MS) stabilizes discontinuous epitopes by covalently linking nearby residues in the antibody-antigen complex with bifunctional reagents, followed by enzymatic digestion and MS identification of interlinked peptides to map spatial proximities.^[50] These techniques balance precision and practicality: crystallography and cryo-EM yield definitive 3D structures but demand significant time and sample optimization, whereas mutagenesis and arrays offer rapid, scalable insights yet may overlook subtle conformational nuances.^[51]

Computational and Predictive Methods

Computational methods for epitope mapping leverage bioinformatics algorithms and machine learning to predict potential antigenic sites without extensive laboratory experimentation, enabling rapid screening of large protein sequences or structures. These approaches typically integrate sequence analysis, structural modeling, and predictive scoring to identify linear or conformational epitopes recognized by B-cells or T-cells. Sequence-based tools focus on amino acid properties and patterns, while structure-based methods incorporate three-dimensional conformations, often drawing from databases like the Immune Epitope Database (IEDB), which curates over 2.2 million epitopes from experimental literature to train and validate models.^[52] Sequence-based prediction methods analyze primary protein sequences to forecast linear B-cell epitopes or MHC-binding peptides for T-cell responses. BepiPred, introduced in 2006, uses a hidden Markov model combined with a propensity scale derived from known epitopes to score residues for antigenicity, achieving improved sensitivity over earlier hydrophilicity-based tools. For T-cell epitopes, NetMHC employs artificial neural networks trained on binding affinity data to predict peptide interactions with specific MHC class I alleles, classifying binders as those with IC50 values below 500 nM, a threshold indicating high-affinity interactions. These tools facilitate initial epitope scanning in pathogen proteomes, prioritizing candidates for further analysis.^[53]^[54] Structure-based methods extend predictions by incorporating protein 3D geometry, often integrating IEDB data for benchmarking against experimentally validated epitopes. Conformational epitope modeling frequently employs molecular dynamics simulations to explore dynamic interactions, with tools like Rosetta using energy-based docking to compute scores for antibody-antigen complexes, such as interface energies that quantify binding stability. Recent integrations include AI-based structure prediction tools like AlphaFold for modeling unbound antigens and complexes, enhancing predictions for cases without experimental structures. ElliPro, a structure-based predictor, assesses epitope likelihood by calculating residue protrusion indices from an ellipsoid approximation of the antigen surface, combined with propensity scores, to identify clusters of solvent-exposed residues likely to form discontinuous B-cell epitopes. These approaches are particularly useful for antigens with available crystal structures, enhancing accuracy for non-linear epitopes.^[55]^[56]^[57]^[58] Machine learning has evolved from early support vector machine (SVM) models, which classified epitopes based on physicochemical features like hydrophobicity and flexibility, to deep learning architectures trained on IEDB datasets for more nuanced predictions. SVM-based tools, such as those in the BCPreds suite from around 2006-2010, achieved moderate performance by mapping sequence windows to epitope/non-epitope labels, while modern integrations, including deep learning models developed through 2025, incorporate convolutional neural networks and more advanced architectures for feature extraction from aligned sequences. ElliPro exemplifies hybrid ML by scoring 3D protrusions, with epitope predictions weighted by geometric and sequence propensities derived from IEDB-curated structures. Training on diverse IEDB entries, including over 10,000 B-cell epitopes, allows these models to generalize across pathogens, though they emphasize linear predictions with AUC values around 0.7-0.8.^[59]^[56]^[60]^[58] Typical workflows for computational epitope mapping begin with genome sequencing of a target pathogen, followed by protein translation and fragmentation into overlapping peptides. Tools like NetMHC then perform allele-specific predictions for T-cell epitopes, filtering for high-affinity binders across common HLA alleles to prioritize immunogenic candidates for vaccine design. For B-cell epitopes, sequence-based scans with BepiPred identify linear regions, refined by structure-based docking if models are available, culminating in a ranked list integrated with IEDB for similarity to known epitopes. This pipeline, as applied in T-cell vaccine development, reduces experimental candidates from thousands to dozens, accelerating design for personalized or pan-population immunity.^[61]^[62] Validation of computational predictions requires integration with experimental data, such as ELISA or flow cytometry assays, to confirm binding or immunogenicity. Metrics like area under the ROC curve (AUC) for B-cell tools, including BepiPred versions, typically range from 0.7 to 0.8 on independent test sets from IEDB, indicating reasonable discrimination but highlighting the need for hybrid approaches to achieve higher precision. For instance, combining NetMHC affinity scores with stability predictions improves T-cell epitope ranking, with validated AUCs exceeding 0.75 for select alleles. These benchmarks underscore the predictive power of computational methods while emphasizing their role as complements to wet-lab confirmation.^[63]^[64]^[54]

Challenges and Future Directions

Limitations of Current Approaches

One major technical hurdle in epitope mapping is the difficulty in accurately identifying conformational epitopes, which predominate in native protein structures but require complex techniques like X-ray crystallography or cryo-electron microscopy (cryo-EM) to capture their three-dimensional context.^[65] These methods often fail for membrane proteins or those needing specific lipid environments, as denaturation during preparation disrupts native conformations.^[66] Additionally, T-cell epitope mapping suffers from low throughput due to major histocompatibility complex (MHC) variability, with low peripheral T-cell numbers necessitating pre-expansion that may overlook minor epitopes.^[65] Practical challenges exacerbate these issues, including high costs and limited scalability of experimental approaches; for instance, cryo-EM structure determination typically ranges from $50,000 to $200,000 per project, restricting access for routine use.^[67] Computational predictions, while faster, exhibit low accuracy for discontinuous B-cell epitopes, with many tools achieving Matthews correlation coefficients near zero—indicating performance little better than random—and success rates often below 50% for conformational sites.^[68] False positives are common in both, such as non-specific adsorption in peptide microarrays or biased mutations in deep mutational scanning.^[66] Labor-intensive experimental methods contrast with computational ones' imprecision, as the former demand extensive validation while the latter overlook post-translational modifications like glycosylation.^[51] From a biological and ethical standpoint, epitope mapping can overestimate immunogenicity, potentially leading to vaccine candidates that fail in clinical trials due to unpredicted immune evasion or adverse responses.^[56] Population diversity poses further risks, as human leukocyte antigen (HLA) polymorphisms result in non-responsiveness to T-cell epitopes in 2-10% of individuals (up to 20% in cases like hepatitis B vaccination), complicating broad efficacy and raising equity concerns in diverse populations.^[69] Data gaps persist, particularly in incomplete epitope databases for non-model organisms, where only a fraction of allergens or pathogens have mapped epitopes, limiting generalizability.^[65] Dynamic epitopes influenced by glycosylation or protein folding remain challenging, as current methods rarely account for these modifications, leading to incomplete or misleading mappings.^[66]

Recent Advances and Emerging Technologies

The integration of artificial intelligence (AI) and machine learning (ML) has revolutionized epitope mapping since 2020, enabling rapid and accurate predictions of both linear and conformational epitopes. AlphaFold2, released in 2021, has facilitated high-resolution structure predictions that aid in conformational epitope identification by modeling antigen-antibody complexes with unprecedented accuracy, achieving a median GDT-TS score of 92.4 across CASP14 targets, corresponding to high-accuracy structures often with RMSD below 1 Å. Subsequent releases like AlphaFold3 (2024) have further improved modeling of antigen-antibody complexes, enhancing epitope predictions. Deep learning models, such as those based on protein language models like ProtBERT, have improved epitope scoring, with some achieving area under the curve (AUC) values exceeding 0.85 for B-cell epitope prediction, outperforming traditional sequence-based methods.^[56] These AI-driven tools, including GraphBepi and AbEpiTope-1.0, leverage AlphaFold-predicted structures to enhance antibody-specific predictions, reducing experimental validation needs.^[70]^[71] The COVID-19 pandemic accelerated epitope mapping innovations, particularly for the SARS-CoV-2 spike protein's receptor-binding domain (RBD), which emerged as a key target for neutralizing antibodies in mRNA vaccines like Pfizer-BNT162b2. Cryo-electron microscopy (cryo-EM) structures resolved in 2020 revealed critical RBD epitopes, such as the ACE2-binding site, guiding vaccine design and showing how mutations in variants like Delta and Omicron alter epitope accessibility.^[72] Polyclonal epitope mapping via electron microscopy on vaccines like mRNA-1273 confirmed focused immune responses to RBD, with over 90% of antibodies targeting conserved sites for broad neutralization. These efforts expanded the Immune Epitope Database (IEDB), which now includes over 1.6 million epitope records as of 2024, incorporating SARS-CoV-2 data to support variant surveillance.^[73] Emerging technologies have further advanced T-cell and functional epitope discovery. Single-cell sequencing, combined with T-cell receptor profiling, enables high-throughput identification of rare antigen-specific T cells, as demonstrated in 2024 methods like TCR-MAP, which map MHC class I- and II-restricted epitopes across thousands of candidates.^[74] Nanoscale imaging via atomic force microscopy (AFM) allows real-time observation of antibody-antigen binding dynamics at the single-molecule level, revealing epitope conformational changes with sub-nanometer resolution.^[75] CRISPR-based approaches facilitate functional mapping by editing putative epitopes in cellular models, validating immunogenicity in vivo, such as in viral antigen screens.^[76] Hybrid methods combining experimental and computational techniques address dynamic epitopes. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) integrated with AI, as in AI-HDX and HDXRank frameworks, predicts epitope solvent accessibility and dynamics, achieving up to 95% alignment with experimental data for flexible regions.^[77] These approaches overcome limitations in static predictions by modeling transient interactions. Looking ahead, recent advances pave the way for personalized medicine through patient-specific epitope mapping, tailoring therapies like neoantigen vaccines for cancer based on individual HLA profiles.^[78] Efforts toward universal vaccines emphasize conserved epitopes, such as those in SARS-CoV-2 GPC proteins, to elicit broad protection against evolving pathogens.^[79]

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Epitope mapping revealed that all of the five mAbs recognized a novel linear epitope located on the glycan loop of E protein domain I. Sequence ...
[39]
Outer surface protein C peptide derived from Borrelia burgdorferi ...
Jan 30, 2013 · We identified a highly conserved 20-amino-acid peptide epitope, OspC1. Via ELISA, OspC1 detected specific IgM and/or IgG in 60 of 98 serum samples (62.1%)Missing: surveillance | Show results with:surveillance
[40]
Multi-Epitope Vaccine Design Using an Immunoinformatic Approach ...
Jun 11, 2021 · An in silico approach based on the viral genome was applied to identify 19 high-immunogenic B-cell epitopes and 499 human leukocyte antigen (HLA)- ...
[41]
A naturally protective epitope of limited variability as an influenza ...
Sep 21, 2018 · The identification of epitopes of limited variability offers a mechanism by which a universal influenza vaccine can be created; these vaccines ...
[42]
Epitope Mapping of Antibody-Antigen Interactions with X-Ray ...
X-ray crystallography is considered to be the gold standard of epitope mapping as it can provide a near atomic resolution model of the antibody-antigen ...Missing: review | Show results with:review
[43]
Cryo-EM model validation recommendations based on outcomes of ...
Feb 4, 2021 · Models derived from single particle cryo-EM maps have increased dramatically since the 'resolution revolution' circa 2014. Higher-resolution ...<|separator|>
[44]
High-Resolution Epitope Mapping of hGH-Receptor Interactions by ...
A strategy, called alanine-scanning mutagenesis, was used to identify specific side chains in human growth hormone (hGH) that strongly modulate binding to the ...
[45]
Epitope Mapping of Polyclonal Antibodies by Hydrogen–Deuterium ...
Jul 24, 2021 · Here we show how hydrogen–deuterium exchange mass spectrometry (HDX-MS) can be used to map epitopes recognized by pAb samples.Experimental Section · Results and Discussion · Supporting Information
[46]
A high-throughput shotgun mutagenesis approach to mapping B-cell ...
Shotgun mutagenesis epitope mapping enables mapping of both linear and conformational epitopes at amino-acid resolution directly within cells, even for the most ...
[47]
High-resolution Mapping of Linear Antibody Epitopes Using ... - NIH
Some information on the biology of antibody recognition of linear epitopes can be extracted. The lengths of the epitopes were mostly 7 to 9 amino acids long ( ...
[48]
Mapping Epitopes by Phage Display - SpringerLink
8 sept 2023 · Phage display is a versatile technology that allows the display of a library of oligopeptides or fragments from a single gene product on the phage surface.
[49]
Epitope Mapping Using Yeast Display and Next Generation ...
Here, we describe a method to precisely and efficiently map the epitopes of multiple antibodies in parallel over the course of just several weeks.
[50]
https://pmc.ncbi.nlm.nih.gov/articles/PMC7501946
[51]
Full article: Epitope mapping of monoclonal antibodies
Nov 27, 2023 · The gold standard of epitope mapping, X-ray crystallography, requires a high degree of proficiency with no guarantee of success. Here, we ...
[52]
Immune Epitope Database (IEDB): 2024 update - Oxford Academic
Nov 18, 2024 · The IEDB team manually curates data from the literature into a structured format and spans infectious, allergic, autoimmune, and transplant diseases.Abstract · Introduction · Search interface · Future plans
[53]
Improved method for predicting linear B-cell epitopes - PMC
The improved method, BepiPred, combines a hidden Markov model with a propensity scale method, and is a novel method for predicting linear B-cell epitopes.
[54]
NetMHCpan, a method for MHC class I binding prediction beyond ...
We present NetMHCpan-2.0, a method that generates quantitative predictions of the affinity of any peptide–MHC class I interaction.
[55]
The Immune Epitope Database and Analysis Resource: From Vision ...
Mar 15, 2005 · Our goal is the creation of the Immune Epitope Database and Analysis Resource (IEDB). The IEDB is sponsored by the National Institute for ...
[56]
Modeling and docking antibody structures with Rosetta - PMC - NIH
We describe Rosetta-based computational protocols for predicting the three-dimensional structure of an antibody from sequence (RosettaAntibody) and then docking ...
[57]
ElliPro: a new structure-based tool for the prediction of antibody ...
ElliPro is considered a useful research tool for identifying antibody epitopes in protein antigens. ElliPro is available at http://tools.immuneepitope.org/ ...
[58]
Recent advances in B-cell epitope prediction methods - PMC
Nov 3, 2010 · B-cell epitopes typically belong to one of two classes: linear (continuous or sequential) epitopes or conformational (discontinuous) epitopes.Missing: paper | Show results with:paper
[59]
Machine Learning Techniques for the Prediction of B-Cell and T-Cell ...
This paper presents a systematic review of various state-of-the-art and relevant ML-based methods and tools for predicting T- and B-cell epitopes.<|separator|>
[60]
T Cell Epitope Prediction and Its Application to Immunotherapy
Sep 14, 2021 · Besides integrating DNA and RNA data, it is also possible to predict neoepitopes from peptide and RNA sequencing data.
[61]
EpiCurator: an immunoinformatic workflow to predict and prioritize ...
This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools.
[62]
BepiPred‐3.0: Improved B‐cell epitope prediction using protein ...
In this paper, we present BepiPred‐3.0, a sequence‐based epitope prediction tool that, by exploiting LM embeddings, greatly improves the prediction accuracy for ...
[63]
BepiPred-2.0: improving sequence-based B-cell epitope prediction ...
May 2, 2017 · We evaluated the performance for each antigen in terms of the area under the receiver operation curve (AUC), the area under the first 10% of the ...
[64]
Potential and limitations of epitope mapping and molecular targeting ...
Dec 14, 2023 · As reviewed by Potocnakova et al. (19), epitope mapping methods are expensive, labor-intensive, time-consuming and often do not identify all ...
[65]
Massively-multiplexed epitope mapping techniques for viral antigen ...
Sep 24, 2023 · Here, we briefly introduce the principles, advantages, and disadvantages of the latest epitope mapping techniques with examples for viral antigen discovery.
[66]
Cost-Benefit Analysis Of Establishing A Cryo-EM Facility
Aug 27, 2025 · ... structural data, with typical commercial cryo-EM structure determination projects ranging from $50,000 to $200,000 depending on complexity.
[67]
Assessing the predictive ability of computational epitope ... - NIH
Our findings show the limitations of current computational epitope prediction methods in accurately identifying allergenic epitopes, emphasizing the need for ...
[68]
AI-driven epitope prediction: a systematic review, comparative ...
Aug 30, 2025 · Integrating AI into epitope prediction is transforming vaccine design by delivering unprecedented accuracy, speed, and efficiency.
[69]
Influence of HLA Class II Polymorphism on Predicted Cellular ...
Non-responsiveness affects approximately 2-10% (and up to 20% following hepatitis B vaccination) of vaccinated healthy individuals (52, 53). HLA class II ...
[70]
Identifying B-cell epitopes using AlphaFold2 predicted structures ...
Based on the recent breakthrough of AlphaFold2 in protein structure prediction, we propose GraphBepi, a novel graph-based model for accurate B-cell epitope ...Missing: ML ProtBERT
[71]
AbEpiTope-1.0: Improved antibody target prediction by use of ...
Jun 13, 2025 · We present AbEpiTope-1.0, a tool for antibody-specific B cell epitope prediction, using AlphaFold for structural modeling and inverse folding for machine ...Missing: ML AlphaFold2 ProtBERT
[72]
EMDB < EMD-48197 - EMBL-EBI
Here we examined the antigenicity of two of the original COVID-19 vaccines, mRNA-1273 and NVX-CoV2373, by electron microscopy-based polyclonal epitope mapping ( ...<|separator|>
[73]
The Immune Epitope Database (IEDB): 2024 update - PMC - NIH
Nov 18, 2024 · The IEDB inserts custom nodes and synonyms to make the hierarchy more 'immunologist friendly.' Additionally, we prune out intermediate nodes, ...
[74]
High-throughput discovery of MHC class I- and II-restricted T cell ...
Jul 2, 2024 · Here we present TCR mapping of antigenic peptides (TCR-MAP), an antigen discovery method that uses a synthetic TCR-stimulated circuit in immortalized T cells.
[75]
Recent advances in the application of atomic force microscopy to ...
The application of atomic force microscopy (AFM) for functional imaging and manipulating biomolecules at all levels of organization has enabled great progress ...Missing: epitope | Show results with:epitope
[76]
[PDF] Massively-multiplexed epitope mapping techniques for viral antigen ...
Sep 25, 2023 · An epitope, the smallest structural and functional unit of an antigen, binds specifically to an antibody or antigen receptor, to serve as key ...
[77]
HDXRank: A Deep Learning Framework for Ranking Protein ...
May 14, 2025 · We developed HDXRank, a graph neural network (GNN)-based framework for candidate structure ranking utilizing alignment with HDX experimental data.
[78]
T-Cell Epitope-Based Vaccines: A Promising Strategy for Prevention ...
Oct 17, 2024 · T-cell epitope-based vaccines have become promising prophylactic and therapeutic tools against infectious diseases that cannot be controlled via traditional ...
[79]
Comprehensive Analysis of the Immune Response to SARS-CoV-2 ...
This study identified highly conserved and evolutionarily constrained SARS-CoV-2 epitopes, which could be crucial for broad-spectrum vaccine development.