High-resolution epitope mapping with >95% success, even for complex proteins and conformational epitopes

>95% Success rate
1,000+ Epitopes mapped

170+ Publications & Patents

How will epitope data help you?

High-resolution epitope mapping enables 1) lead candidate selection by uncovering mechanisms of action and 2) MAb protection by strengthening IP

Epitopes Differentiate Mechanism of Action

Epitope Maps Strengthen Intellectual Property

What makes our epitope mapping platform better?

Integral Molecular’s proprietary Shotgun Mutagenesis technology is the only high-throughput technique that can reliably map conformational epitopes at single amino acid resolution

We have mapped 1,000+ epitopes to date with >95% success, including:

  • Epitopes on GPCRs, transporters, and viral envelope proteins
  • Conformational epitopes
  • Epitopes on multi-subunit proteins
  • Receptor state-dependent epitopes

"The epitope mapping that Integral Molecular has done has greatly supported both our mechanistic understanding and the intellectual property claims of our proprietary antibodies."

How do we achieve a >95% success rate?

Using our high-throughput Shotgun Mutagenesis platform, we mutate each residue of a target protein and measure the precise binding of an antibody to the target within intact cells

Shotgun Mutagenesis Epitope Mapping:
  • Automated point mutation of every residue in the target protein to alanine
  • Native expression of each protein mutant in human cells
  • Native expression of individual mutants in human cells, enabling mapping of conformational epitopes
  • High-throughput expression, antibody reactivity, and functional testing
  • 3D structural visualization of the epitope

What epitope mapping services do we offer?

Epitope mapping services are provided on a fee-for-service basis, and Integral Molecular provides access to all final data to enable regulatory and intellectual property filings

Antibody Epitope Mapping Services

An Ala-scan mutation library is created for the protein target of interest and used to test binding of customer’s MAbs/ligands by flow cytometry to identify epitope residues

Expedited ReadyMap Epitope Mapping Services

Expedited epitope mapping is available on full-length, pre-constructed and pre-validated ReadyMap libraries for quicker lead selection
Please see current ReadyMap Library offerings below
Additional ReadyMap libraries launching soon

Mapping Small Molecule Binding Sites

Small molecules are screened on the library using functional assays to identify amino acid residues that are critical for binding or function

ReadyMap: Available Protein Targets

Pre-constructed and pre-validated libraries for quicker turnaround

Updated regularly with new targets

Protein Class
Protein Target
Chemokine receptor
Chemokine receptor
Leucine-rich repeat-containing G-protein coupled receptor 5, stem cell marker
ADP-ribosyl cyclase
CD137 (TNFSR9)
TNF superfamily receptor
Immune checkpoint
Immune checkpoint
Receptor Tyrosine kinase
HER2 (ErbB2)
EGFR family
Receptor Tyrosine kinase
HER3 (ErbB3)
EGFR family
Viral Protein
DENV prM/E Serotypes 1-4
Dengue virus envelope proteins
Viral Protein
Zaire ebolavirus envelope glycoprotein
Viral Protein
Marburg virus envelope glycoprotein
Viral Protein
Hepatitis B Virus surface antigen
Viral Protein
Hepatitis C virus envelope proteins
Viral Protein
Respiratory syncytial virus fusion protein
Viral Protein
SARS-CoV-2 S1, S2
SARS-CoV-2 Spike protein, including RBD, NTD, S2
Viral Protein
Zika virus envelope proteins

Epitope Mapping Projects Include:

  • Assay Setup Report, summarizing optimized conditions for screening
  • MAb/ligand screening on the Ala-scan mutation array
  • Final report, containing:
      • 1. Fully analyzed data package
      • 2. Identification of amino-acid resolution epitope
      • 3. Publication-ready figures

170+ Epitope Mapping Publications & Patents

Featured Case Studies

Novartis characterized mechanism of action for CXCR2 nanobodies

Covagen distinguished HER2 antibodies from existing therapeutics

Learn how epitope mapping enhances antibody patent protection

"Integral Molecular was able to identify critical binding residues for an antibody for which no mapping had been successfully done after years in development."

"Excellent team, excellent communication, results when promised, results with impact to drive decision making."

Frequently Asked Questions

Our epitope mapping approach utilizes Shotgun Mutagenesis, a proprietary platform for high-throughput alanine-scanning mutagenesis. We create a comprehensive mutagenesis library by mutating each residue of the full-length target protein to alanine. Next, each variant is expressed by live human cells within individual wells of a 384-well plate. Using high-throughput flow cytometry, we determine the binding of your antibody to each variant. Mutated positions that no longer support antibody binding are identified as putative epitope residues. Importantly, our platform includes critical controls to ensure that identified residues are part of the epitope rather than artifacts. To date, our Shotgun Mutagenesis Epitope Mapping platform has been used to identify 1,000+ epitopes with a >95% success rate, even for conformational antibodies and highly complex proteins.

Shotgun Mutagenesis Epitope Mapping can be used to identify both linear and conformational epitopes at amino-acid resolution, even for complex, multipass membrane proteins. By contrast, peptide mapping determines antibody binding to short peptides, independent of protein tertiary structure, precluding its use for mapping conformational epitopes. Compared to H/D exchange, Shotgun Mutagenesis Epitope Mapping does not require a soluble or purified form of the target protein. Cryo-EM can be time-consuming and expensive, and requires large quantities of correctly folded and natively processed target protein. Shotgun Mutagenesis Epitope Mapping is suited to mapping antibody epitopes on any protein target, including GPCRs, ion channels, and proteins with complex folds, such as immuno-oncology targets, without the need for protein purification or high cell surface expression.

Control antibodies are used to validate that the mutated protein exhibits proper trafficking, expression, and folding. Typical control antibodies include commercially available reagent antibodies or the customer’s noncompeting antibody against the same target. If a control is not available, then an epitope-tag (FLAG, V5, HIS6, etc.) can be added to the target protein and used to control for expression and trafficking. In some cases, we use the function of the target protein as a control for proper folding.

The deliverables for a project are an Assay Setup Report and a Final Report containing publication-ready figures. The Assay Setup Report is delivered before initiation of mutagenesis and determines the optimal high-throughput antibody screening conditions, which are established by using a wild-type protein construct. Upon completion of the mapping project, a Final Report is delivered. This report includes a graphical representation of the data, identities of the critical interacting residues, and a structural representation of the epitope mapped on the target protein. As part of the project, Integral Molecular assists customers in preparing high-quality figures or tables for publications, presentations, and patent/regulatory filings.

A Shotgun Mutagenesis Epitope Mapping project can be initiated on any protein that can be expressed in cells, including soluble proteins and conformationally complex proteins, such as GPCRs, ion channels, transporters, and viral envelope proteins.

Custom epitope mapping projects typically take 3-4 months from project initiation to receipt of the Final Report. ReadyMap projects typically take 4–6 weeks. Please contact us to discuss your project. A more accurate timeline will be established after initial discussions.

To begin an epitope mapping project, we require the sequence of the target protein and 500 µg of each antibody that will be mapped.

Ready To Get Started?

We have worked with more than 100 top biotech and pharmaceutical companies to help them succeed. Let’s talk about how we can help you.

Or call (215) 966-6061