DiscoTope-3.0 predicts the epitope propensity of input protein structures.

Instructions

The server requires input protein structures in the PDB format. These may either be uploaded by the user or downloaded by the DiscoTope-3.0 server.

Choose between either:

1. Upload a protein PDB structure or a compressed ZIP archive with the Choose file button (arrow A). The ZIP file may contain up to 50 PDBs. The chosen file may not be larger than 30 MB.
2. Enter a list of protein structure IDs, to download from either RCSB or AlphaFoldDB based on the flag set in arrow C. No chain specification should be used (e.g. 5d8j_A). Up to 50 IDs may be given, with one ID per line.

After providing one of the two input options, specify the input structure type (arrow C). Experimental PDB structures (solved) and AlphaFold2 predicted structures are supported.

Finally, click submit to complete the submission (arrow D).

DiscoTope-3.0 output

DiscoTope-3.0 outputs single chain PDB files, with matching per-residue CSV files

Use the drop-down menu (arrow A) to switch the view to another predicted PDB chain among all provided PDB files.

The selected chain is visualized in an interactive view below using Mol* (arrow B). This view may be rotated freely (click and move), along an axis (hold shift), zoomed (scroll) or moved (hold ctrl) using the mouse and listed keys in parantheses.

Move the cursor over a residue to see it's predicted DiscoTope-3.0 score, residue ID as well as the chain name (arrow C). Residues with higher epitope propensity are colored in a deeper red, while residues with lower epitope propensity are colored in a deeper blue. The color scale is absolute and not adjusted per PDB.

All output predictions may be downloaded as a compressed ZIP archive (arrow D), containing per PDB chain predictions in both .CSV and .PDB format.

Single PDB chain results may be downloaded in a .CSV or .PDB format by clicking the "Individual result downloads" button (arrow E).

The CSV files contains per-residue outputs, with the following column headers:

• PDB ID and chain name
• Relative residue index (re-numbered from 1)
• Amino-acid residue, 1-letter
• DiscoTope-3.0 score
• Relative surface accessibility (Shrake-Rupley, normalized using Sander scale)
• AlphaFold pLDDT score (set to 100 for non-AlphaFold structures)
• Chain length
• A binary feature set to 1 for AlphaFold structures.