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After you have edited a ligand and re-docked or minimized it you can evaluate the Score and Strain for the ligand. Ideally a good modification to your ligand will lower the score.
About the Score
- LE_Score The lower the Score the better the predicted interaction.
- RTCNN (Radial Topological Convolutional Neural Net) - you can read more about this score here. The lower the better the predicted interaction.
- LigStrain = The strain of the ligand. Lower values = less strain.
About the Score in ICM versions older than 3.9
- 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. This score does not incorporate the strain of the ligand compared to the free state.
- LigStrain = The strain of the ligand. Lower values = less strain.
- Score = This score does incorporate ligand strain. Therefore it is VlsScore + LigStrain. The lower the Score the better the predicted interaction.
To evaluate the Score and Strain:
- Click on the "Recalculate Binding Score Button".
About Strain If your docked ligand is strained e.g strain >3 then there are some things you can do to investigate the reason for this.
- Look at the relaxed ligand in the ligand editor - are there significant differences between relaxed and docked ligand
- Display the energy circles - does that give any clues. This will display simple torsion circles visualization is limited to localized torsion strain such as amide bonds twisted out of plane.
- Another way to discover where the strain stems from is to perform constrained cartesian relaxation (minimization) of the ligand and observe resulting movements:
- Make a copy of the ligand (molecule drop-down menu in workspace/Copy to another object)
- Make the copy current (object drop-down/Set to current)
- Perform minimization (Menu MolMechanics/Minimize/Cartesian)
Note that sometime strain is "global" i.e. it originates from the existence of a significantly lower energy conformer that is substantially distinct from the bound conformation. This is not readily visualizable, but can be better understood via conformational analysis of the free ligand (i.e. menu Chemistry/Generate 3D Conformers…) and comparison of the bound conformation to the energy spectrum of free conformers. <>
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