Why is there always a small difference between the score calculated interactively by scanScoreExternal and that obtained by docking (VLS)?
The reason for this is that ICM score has terms that require calculations on the reference ‘free’ state of the ligand, in particular solvation electrostatics and internal force-field strain energy change are calculated as a difference between free and bound state. VLS uses as a free state the lowest energy conformation found by MC search for the unbound ligand. Interactive score just minimizes the ligand locally. To ensure consistency we recomend you use one method or the other for scoring or you could recalculate the interactive score for your ligand from VLS before modifying/minimizing.
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