IndiskaAI Logo
Back
Antibody Discovery / Epitope Analysis

Explore Potential Antibody Binding Sites.

Investigate where an antibody may interact with its target using available structural and computational evidence.

Discuss an Epitope Analysis →Explore the Analysis Workflow
  • Heavy chain· chain H
  • Light chain· chain L
  • Hen egg-white lysozyme· chain Y
  • Interface residues (< 4.5 Å)

A real interface. HyHEL-10 Fab bound to hen egg-white lysozyme, rendered live from PDB 3HFM. The 18 antigen and 20 antibody residues in gold, and every distance the scene names, are computed from the deposited coordinates. Drag to turn it.

A worked example of what an interface looks like, not a result from your target. This complex was solved experimentally; a region suggested computationally on a new antigen is a hypothesis until it is tested.

Where on the antigen might an antibody bind?

An epitope is the region of an antigen recognized by an antibody. Computational analysis can suggest potential regions using available structural or predicted interface information. These predictions require appropriate interpretation and, where confirmation is needed, experimental mapping.

The analysis workflow

Select a stage. Not every project includes every stage.

Antibody and target information

Purpose
Establish what is known about the target and the antibody.
Information used
Target sequence and/or structure. Antibody sequence, or an antibody–target complex, where available.
Analysis
Which inputs are usable and what question the analysis should address.
Possible output
A confirmed input summary.

Limitation. Missing inputs limit which later stages can run.

Explore Residue-Level Evidence

A real antibody–antigen complex, with every residue, distance and contact class computed from its deposited coordinates. Select a residue on the antigen to see what it contacts.

Show

HyHEL-10 Fab and hen egg-white lysozyme, rendered live from PDB 3HFM. The scene cycles through the contact pairs it computes from the coordinates and names each one. Drag to turn it.

Antigen interface residues · chain Y

18 within 4.5 Å

Dashed outlines sit inside 4.5 Å of the antibody but have no atom pair within the 4 Å contact window, so they are interface residues with no contact to report.

Residue evidence

Arg 14 · chain Y

Contacts within 4 Å
  • Asn 31Light chain3.7 Åvan der Waals
How this was measured
Atom pairs between chain Y and chains H/L in the deposited structure. Interface below 4.5 Å, contacts between 2.3 and 4 Å. These are this analysis’s configured thresholds, not a definition of an epitope.
What “polar” means here
Both atoms are nitrogen or oxygen and lie within 3.5 Å. The coordinates carry no hydrogens and no angle criterion is applied, so this is consistent with a hydrogen bond or salt bridge rather than proof of one.
Status
Observed in an experimentally determined complex. A region suggested computationally on a new antigen is a hypothesis, and needs experimental mapping to become a confirmed epitope.

What a supplied complex supports

The residues and distances shown are measured in the deposited structure. They describe one molecular configuration and the proximities within it. They do not, on their own, establish affinity, specificity or biological function.

Structural proximity, an identified contact type, a predicted interface and experimental confirmation are four different things. This panel shows the first two.

From Inputs to Insights

  • Target protein sequence and/or structurerequired in some form
  • The research questionrequired
  • Antibody sequence or antibody–target complexoptional
  • PDB or mmCIF files, if supportedoptional
  • Relevant experimental binding informationoptional

What is needed depends on the workflow. Optional items allow more of it to apply.

Explore related services

Want to examine a potential binding site?

Share your target, any structures and what you need to know. We will discuss the analysis.

Discuss an Epitope Analysis →