Epitope Visualizer

This tool visualizes IEDB epitope data on 3D protein structures. Load an antigen by entering a PDB ID, then upload an epitope CSV file to highlight immunogenic residues directly on the structure.

A built in dataset is included with epitopes automatically highlighted as a demonstration. The SARS-CoV2 spike protein (UniProt: P0DTC2) was searched in IEDB and mapped onto the most complete structure identified in UniProt (PDB: 6VSB). Additionally, the suggested 319 start & 541 end positions are the range of the RBD domains, region of high research interests.

This project was originally developed as part of the epitope visualization project in github prior to it's integration here as a demonstration. See the github link for the original python functions and how they can be applied in pymol.

Quick Start
  1. Find antigen in UniProt — Search for antigen in Uniprot database.
  2. Select PDB structure — Identify PDB ID of interest within 'structure' section of UniProt entry
  3. IEDB search — Use UniProt ID to search for DISCONTINUOUS EPITOPES ONLY in IEDB & export results as single header CSV file.
  4. Load a structure — Enter a PDB ID (default: 6VSB) and click Load.
  5. Add epitope data — Upload IEDB CSV file, or click Reload Default to use pre-loaded SARS-CoV-2 Spike epitopes.
  6. Highlight — Click Highlight All Epitopes to color every epitope residue, or Highlight Epitopes in Selection to restrict to a Start/End range.
  7. Explore — Click and drag to rotate, scroll to zoom. Switch styles or toggle the background to suit your view.
  8. Save — Click Screenshot to download the current view as a PNG.


Practice search - Follow instructions to load Hemagglutinin using UniProt: P03452 and PDB: 1RU7.

Load Data

Antigen of Interest PDB ID:


Adjust Visualizer Settings

Style:

Click and drag to rotate. Scroll to zoom.