How to identify binding site of E3 ligase and target?

[kelly1210]

I have tried the PROTAC docking, but there is a little of problem that the docking structures staggered together. So I want to know if is there a strict restriction for the initial conformation of the E3 ligase and target? And need a initial crystal structure of E3 ligase and target?

[danielzaidman]

Hi, I'll be happy to try to help. But unfortunately I didn't quite understand the question.
Could you please elaborate?
Thanks, Daniel.

[kelly1210]

Hi, I'll be happy to try to help. But unfortunately I didn't quite understand the question. Could you please elaborate? Thanks, Daniel.

OK, Before the PROTAC docking, I think if it is need that HeadA docked to StructureA, and HeadB docked to StructureB, and then we extract the HeadA and HeadB from the docking conformation as the initial sdf files?
And I have another question. I am a little confused to analyze the final results like score.rc file and clustering results. If I just focused on the total_enery and got mean energy value for each compound, I found it is not a good correlation for the PROTAC molecules with different DC50. So I want to know is there a better auto method to sort the compounds?

[LondonLab]

Hi, apologies, I've just seen this message now.
If still relevant, please contact me at [email protected] and I'll try to help.
Best, Daniel.