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In the Docking/Load Example the ligand is not optimally bound to the receptor. A clash between one of the atoms and the receptor is highlighted by an orange star (see below). We can also calculate the binding energy of the receptor complex and Score.
To remove this clash we can re-dock or minimize the biotin ligand. To do this click the "Re-Dock" ligand button.
About the Score
- VlsScore = 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.
- LigStrain = The strain of the ligand. Lower values = less strain.
- Score = VlsScore + LigStrain.
@About the Purple Box:} 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 clicking and dragging on the corners of the puprle box. You will then have to remake the maps by re-clicking the display/modify pocket box.
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