IEDB Analysis Resource

DiscoTope - Tutorial

DiscoTope is a method for predicting discontinuous epitopes from 3D structures of proteins in PDB format (see Reference at the end of the tutorial).
How to use the tool
Step 1.
Enter the structure either by entering its PDB id (Each structure in the PDB is represented by a 4 character identifier of the form [0-9][a-z,0-9][a-z,0-9][a-z,0-9][a-z,0-9]. For example, 4HHB, 9INS are identification codes for PDB entries for hemoglobin and insulin) Or, by uploading a Structure File in PDB format from your computer.
Step 2.
Enter the Chain id for the protein chain of interest. For example, 4HHB PDB structure has four chains, A, B, C, and D. Only one chain can be selected to run through the tool. If you want to predict epitopes in a multi-chain protein, for example, considering the whole oligomer of the hemoglobin (all four chains together), you need to modify a correspondent PDB file (4HHB.pdb) so that all chains of interest have the same chain ID (specified in the column 22 of the ATOM record in the PDB format file). To avoid conflict of residues having the same numbers in the modified PDB file, residues might need to be renumbered.
Step 3.
Select DiscoTope version.
Step 4.
Click on submit.
* Note that version 2.0 has not yet been optimized and will therefore take far longer to process your request than 1.1. For a description of the differences between the versions, please click here.
On the following screen, you will be able to see the predicted discontinuous epitopes as a chart of DiscoTope score vs. residue id. Here, you can change the threshold for predictions, view results in table or 3D viewer, save the prediction result or start with a new prediction.
Chart view
To change the threshold value, enter a different threshold and click on 'Change'. The default value for version 1.1 is -7.7 and version 2.0 is -3.7, which corresponds to a specificity of 75%. Higher values correspond to higher specificity. A specificity of 0.75 means that 25% of the nonepitope residues were predicted as part of epitopes. A sensitivity of 0.47 means that 47% of the epitope residues were predicted as part of epitopes.

In a benchmark containing more than 75 antigen/antibody complexes, the following relations were found:
Score Sensitivity Specificity
>-3.1 0.16 0.95
>-4.7 0.24 0.90
>-6.0 0.32 0.85
>-6.9 0.40 0.80
>-7.7 0.47 0.75
Score Sensitivity Specificity
>1.9 0.17 0.95
>0.5 0.23 0.90
>-1.0 0.30 0.85
>-2.5 0.39 0.80
>-3.7 0.47 0.75
In the chart, predictions above the threshold (red line) are positive predictions (displayed in green) and predictions below the threshold are negative prediction (displayed in orange).
Table view
Table view lists following columns: Positive predictions are displayed in green.
3D view
The 3d view uses Jmol to display the structure with positive predictions highlighted in yellow. The side chain of each predicted residue is shown. You can rotate, zoom and manipulate the structure by using different buttons on the mouse. The table lists the predicted epitope residues along with their chain id, residue id, contact number, propensity score and DiscoTope score. Clicking on the CPK button in each residue will highlight this residue in CPK on the 3D viewer.

[Final version of Discotope 3D img. to follow]