affinity (KCal/mol) values from your Webina predicted docking

[Yutao Qi]

Hi Dr. Durrant,

From my Webina docking, affinity values are positive. Does it mean the possible binding between my ligand and receptor is weak? However, docking indicated that the ligand binds deep into a narrow cavity of the receptor.

Thank you very much!

Best regards,

Yutao

[Jacob Durrant]

Hi Yutao. Much thanks for your interest in Webina. Really this question applies to AutoDock Vina too. I’ve occasionally seen slightly positive scores in some of my virtual screens. These typically correspond to poses that are not correct. It could be, for example, that there are some clashes between the atoms of the posed ligand and one or more atoms of the protein receptor. You might try expanding the size of your docking box or perhaps increasing the exhaustiveness parameter. Best of luck with your project!

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