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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
 Small Molecule Docking
 Flexible Docking
 Template Docking
 Covalent Docking
 Autofit
 Peptide Docking
 Protein-Protein Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
12.6 Peptide Docking
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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-termincal and D-amino acids 0 nter 1 gly 2 ala 2A Dglu 4 asp cooh 

Then 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 in the table side panel and then dock.


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