Modification of a peptide in the Ligand Editor

[MolSoft ICM Knowledge Base]

Question:

I would like to modify a peptide in the ICM 3D Ligand Editor. How can I get ICM to recognize the peptide as a ligand?

Answer:

The ligand editor is primarily for small molecule drugs but it can be used to visualize peptide-receptor interactions and making careful modification to peptides in a binding pocket. To set the peptide as a chemical ligand in the editor:

1. Move the peptide into a separate object by right clicking on peptide in the ICM Workspace and choose "move to separate object".
   
2. Change "pep" in the command line below to the name of your peptide and copy and paste the text into the terminal window.                                                                                                                                        read mol input=String( Chemical( a_pep. exact hydrogen ) ) name="lig"
3. Setup the ligand and receptor in the ligand editor (ligedit) tab.