Peptide Dock

Peptide Dock performs peptide–protein docking simulations to predict the binding poses and molecular interactions of peptide ligands at the active site of a target protein.

Predecessor module

• PDB File Upload
• PDB Code Input
• Peptide Upload
• Peptide Sequence Upload
• PocketFinder
• Peptide Dock
• Peptide Design

Input Parameters

Select an Input module

If you already have a peptide sequence, use the Peptide Sequence Upload module.

Specify the Target Binding Site

Specify the active site of the target protein.
If you used PocketFinder to identify the active site in the previous step, the corresponding coordinates will be entered automatically.❗PocketFinder is optimized for identifying small-molecule binding sites. Therefore, it may not always accurately predict peptide-binding sites. Before running Peptide Dock, verify that the predicted active site is suitable for peptide binding. If necessary, manually specify the active site before proceeding with the analysis.

The uploaded peptide information is displayed.

Module running screen

Progress messages

Result screen