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PrevICM User's Guide
15.9 Dock or Minimize Ligand

[ 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.

15.9.1 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.

Bioisostere Scan
Dock Table

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