ICM GUI Manual

[ Set Up the Docking Project and Receptor | Preparing a Table with Peptide Sequences | Sequence Format Guide | Importing Sequences (Optional) | Docking a Peptide Table ]

|Video Example|

Peptide docking uses a sequence table and a prepared receptor docking project. Prepare the receptor, enter or import the peptide sequences, and then run Docking/Dock Peptide Table.

14.1.1 Set Up the Docking Project and Receptor

14.1.2 Preparing a Table with Peptide Sequences

[ Create a New Table ]

To create a table for peptide sequences, follow these steps:

14.1.2.1 Create a New Table

14.1.3 Sequence Format Guide

[ Standard and Advanced Numbering | Specialized Bonds and Cyclization | Crosslinks and Modifiers | Terminal Designations | Preparing Extended Sequence Syntax for Unusual Amino Acids ]

Before defining sequences, check icmff.res in $ICMHOME (distribution directory) to see which residue types ICM supports. All defined residues are stored in the icmff.res file in the ICM distribution directory. It is a text file so you can view it in a text editor or grep it. Example to search for ornithine grep ornithine icmff.res and you will see the code is 'orn'

For residues not included in the library, see the unusual amino acid section below.

14.1.3.1 Standard and Advanced Numbering

14.1.3.2 Specialized Bonds and Cyclization

14.1.3.3 Crosslinks and Modifiers

Use curly braces {} for crosslinks or unusual modifications.

Note: Modifiers cannot be applied to the backbone (C, Calpha, and N atoms). Hydrogen and side-chain atoms are acceptable.
The terminal amide has to be preserved as backbone but you can create terminal amide to side-chain crosslink via a terminal ‘residue’

e.g. 

… lys{ce_Xa} …. trp cmet{hm1_Xa}

14.1.3.4 Terminal Designations

Terminal Type ICM Residue Code
C-terminal amide conh
N-terminal charged amine nh3+
N-terminal neutral amine nter

Example Input File Sequence:
nh3+ nle ala ala ala ala conh

14.1.3.5 Preparing Extended Sequence Syntax for Unusual Amino Acids

14.1.4 Importing Sequences (Optional)

14.1.5 Docking a Peptide Table

[ Start Docking | Adjusting Docking Parameters (Optional) | Restraining or Biasing the Peptide Structure ]

14.1.5.1 Start Docking

14.1.5.2 Adjusting Docking Parameters (Optional)

14.1.5.3 Restraining or Biasing the Peptide Structure

You can restrain or bias the ligand towards a specific secondary structure. To do this, define each residue with one of the following secondary structure types: