Does FABind provide some confidence/affinity score?

[lindsey98]

Does FABind provide some confidence/affinity score?

[QizhiPei]

Hi lindsey:

Thanks for your interest in our work.
This score you mentioned above is used to decide the probability of a amino acid belonging to the pocket in the data sample (i.e., each protein-ligand pair) level.
However, in the docking problems, all the training samples are protein-ligand pairs with pocket, which means that there are only positive cases and no negative cases in the dataset (i.e., protein-ligand pairs) level.
Therefore, given an arbitrary protein-ligand pair, the pocket prediction model may still output high scores for some amino acid in the proteins.
Currently I do not think there are any available outputs in FABind that can used to decide whether a pair of protein-ligand can bind or not.

[lindsey98]

Thank you for your quick reply!