- ◇ COMPUTATIONAL · 04
ANTIBODY INTERFACE VIA
Epitope Mapping
Physical modelling of molecular motion, interactions and binding-site behavior.
- EPITOPE · Residue-level
Atomic-resolution antibody interfaces.
Epitope mapping characterises the precise binding site of an antibody on its antigen, defining which residues are contacted, what conformational changes occur upon binding, and how the paratope engages the epitope surface. This information is critical for vaccine immunogen design, antibody humanisation, patent differentiation, and prediction of variant escape mutations.
We offer the full spectrum of epitope mapping modalities. Cryo-EM delivers atomic-resolution structures of antibody–antigen complexes, routinely achieving sub-3 Å resolution for Fab or full IgG bound to conformationally sensitive viral surface proteins, receptor ectodomains, and tumour antigens. For larger antibody panels, HDX-MS and competitive binding assays rapidly classify and bin epitopes.
Structural epitope data directly informs vaccine antigen design, antibody affinity maturation, and combination therapy selection, providing the mechanistic foundation needed to explain and predict biological activity.
- ◇ WHAT IT REVEALS
Residue-level contact maps and conformational epitope architecture.
Structural epitope mapping reveals which antigen residues are directly contacted by the antibody, which are conformationally rearranged upon binding, and which are buried within the interface, information that predicts escape mutation risk and guides affinity maturation strategies.
HDX-MS footprinting rapidly identifies which peptide regions show reduced deuterium exchange upon antibody binding, providing epitope bins for entire antibody panels within days and directly complementing high-resolution cryo-EM structures of lead candidates.
- Atomic-resolution contact maps for structure-guided affinity maturation
- Escape mutation risk prediction from interface residue conservation analysis
- Rapid epitope binning of antibody panels by HDX-MS and competitive SPR
- Conformational vs. linear epitope distinction from structural data
- ◇ WORKFLOW
How we work.
- 01
Complex Preparation
Antibody Fab or full IgG production and complex assembly with antigen at defined stoichiometry.
- 02
HDX-MS Footprinting
Deuterium exchange footprinting of antibody-bound vs. free antigen to identify protected peptide regions.
- 03
Cryo-EM Data Collection
High-resolution cryo-EM dataset collection on Titan Krios for atomic-resolution complex structure determination.
- 04
Structure Determination
Single-particle analysis in cryoSPARC with focused classification on the Fab binding interface.
- 05
Interface Analysis
We review predicted poses, interaction patterns, chemical diversity and practical follow-up criteria to select the most relevant candidates.
- 06
Epitope Report
Residue-level epitope map, escape mutation risk assessment, and immunogen design recommendations.
- 01
Complex Preparation
Antibody Fab or full IgG production and complex assembly with antigen at defined stoichiometry.
- 02
HDX-MS Footprinting
Deuterium exchange footprinting of antibody-bound vs. free antigen to identify protected peptide regions.
- 03
Cryo-EM Data Collection
High-resolution cryo-EM dataset collection on Titan Krios for atomic-resolution complex structure determination.
- 04
Structure Determination
Single-particle analysis in cryoSPARC with focused classification on the Fab binding interface.
- 05
Interface Analysis
Contact residue mapping, buried surface area calculation, hydrogen bond and hydrophobic interaction analysis.
- 06
Epitope Report
Residue-level epitope map, escape mutation risk assessment, and immunogen design recommendations.
- ◇ APPLICATIONS
Where this service applies.
Explore how this service is used to address real structural biology challenges across drug discovery, protein engineering, and beyond.
- ◇ FAQ
Epitope mapping questions.
What is computational epitope mapping?
Computational epitope mapping identifies and characterizes potential antibody-binding sites on an antigen using structural modelling and computational analysis. By analysing the predicted antibody–antigen interaction, we can provide insights into the location and molecular characteristics of the epitope without requiring an experimentally determined complex structure.
What do you need to perform computational epitope mapping?
We typically require the amino acid sequences of the antibody and antigen. If experimentally determined structures or existing high-quality models are available, these can also be incorporated into the analysis. We assess the available data and select the most suitable computational workflow for your system.
Can you perform epitope mapping if no experimental structure is available?
Yes. When no experimental structure is available, structural models of the antibody and antigen can be generated and used as the basis for the analysis. Computational modelling can therefore provide an early structural hypothesis of the binding mode and epitope before experimental structure determination is available.
What information can computational epitope mapping provide?
The analysis can identify the predicted binding region on the antigen, residues likely to contribute to the antibody–antigen interface, and the overall geometry of the interaction. These insights can help explain antibody specificity and support the comparison and characterization of different antibody candidates.
How reliable are computational epitope predictions?
The reliability of a computational epitope prediction depends on the quality of the available structural information and the characteristics of the antibody–antigen system. Computational results should therefore be considered structural hypotheses rather than direct experimental evidence. We evaluate the confidence of the models and communicate relevant limitations as part of the analysis.
When should I use computational instead of experimental epitope mapping?
Computational epitope mapping is particularly valuable when structural insights are needed quickly, when an experimental complex structure is not yet available, or when several antibody candidates need to be assessed and prioritized. For projects requiring direct structural confirmation of the antibody–antigen interface, computational analysis can also be combined with experimental structural biology.
Can computational epitope mapping support antibody development?
Yes. Understanding where and how an antibody is predicted to bind can support antibody selection, differentiation of candidates, interpretation of functional data, and subsequent antibody engineering. Computational epitope mapping can therefore provide actionable structural information at multiple stages of antibody discovery and development.
- ◇ RESOURCES & DOWNLOADS
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