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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
Virtual Screening
MolScreen
3D Ligand Editor
 Setup Ligand and Receptor
 Preferences
 Display Options
 Score and Strain
 Edit Ligand
 Screen Replacement Group
 Scan
 Dock or Minimize
  Expand Pocket
 Dock Table
 Fragment Linking
 Restraints
 Docking Templates
 Flexible Groups
 Refinement
 Multiple Receptor Docking
 Covalent Docking
 Dock to APF
 Save Docked Complex
 Export Docking Project
 Close Project
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
15.8 Dock or Minimize Ligand
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[ Expand Pocket ]

Available in the following product(s): ICM-Pro | ICM-VLS | ICM-Chemist-Pro

Video |

How to Dock or Minimize a Ligand in the Grid maps:

  • Setup the ligand and receptor.
  • Click on the dock or minimize button (see image above).
  • Check the Score and Strain in the top right panel.

If you dock a chemical spreadsheet will be displayed with the docking results. Use the check box in column 'L' to display the docked ligand or double click to load the ligand into the ligand editor.

A guide to the table columns:

  • Score: This score does not incorporate ligand strain. Therefore it is VlsScore - LigStrain. The lower the Score the better the predicted interaction.
  • VLS Score: The ICM-VLS score used for ligand screening. The lower the Score the better the predicted interaction. VLS score is available with ICM-Pro + VLS and ICM-Chemist-Pro products. This score incorporates the strain of the ligand compared to the free state.
  • Strain: The strain of the ligand. Lower values = less strain. (kcal/mol)
  • Steric: Is the van der Waals interaction energy (sum of gc and gh van der waals). Current version of the score uses explicit van der Waals interaction energy calculation (no grids). (lower the better)
  • Torsion: Number of torsions in ligand
  • Electro: is the solvation electrostatics energy change upon binding (lower the better)
  • Hbond: is Hydrogen Bond energy - (lower the better)
  • Hydroph is the hydrophobic energy in exposing a surface to water (lower the better)
  • Surface is the desolvation of exposed h-bond donors and acceptors (lower the better)

How to undertake an all-atom minimization in cartesian coordinates:

  • Note this option is available in ICM 3.8-4 and higher.
  • Click and hold on the Minimize button.
  • Choose Minimize in Receptor.

15.8.1 Change the Size of the Docking Region


How to change the size of the docking region:

The purple box represents the region in which the energy maps are generated. If you want to change the size of this region you can do so by displaying the box (go to Advanced menu) and clicking and dragging on the corners of the puprle box. The maps will then be remade on the fly.


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