To dock a peptide to a protein structure:

• Setup the protein receptor the same way you would for small molecule docking.
• Prepare a table containing one or more peptide sequences. You can do this by going to File/New and choose the table tab. Then choose one string column and the number of rows (peptides you wish to dock). The table could also be read in from Excel or csv format. Or you can extract a peptide sequence from a peptide you have read in from the PDB - right click on the pepetide and choose 'Extract Sequences to Table'.
• Then you will see a new table. Edit the column name to 'sequence' and enter your peptide sequence. You can enter the sequence as shown below:

• gly ala ser pro tyr his
• or more advanced with numbering, N- and C-terminal and D-amino acids 0 nter 1 gly 2 ala 2A Dglu 4 asp cooh

To dock the ligand:

• Docking/Dock Peptide Table - click OK if you want to use the default docking settings. If you uncheck 'dock immediately' you will be able to change the thoroughness and number of conformations using the options in the table side panel and then dock. There is also an option to restrain or bias the ligand to a particular secondary structure. You will need to define each residue by the secondary structure type "H" - alpha helix, "G" - 3/10 helix, "I" - pi helix, "E" - beta strand, "B" - beta-bridge, "_" - undefined or "C" - coil