[Dock-fans] Amber score "divide & conquer"

[John J. Irwin]

Hi Francesco

Francesco Pietra wrote:
> I am sampling a big protein for small_molecule docking by creating
> selected_spheres/boxes for parts of the protein. Grid for the whole
> protein would be too big. Also,e creating models for parts is
> difficult because each chain lengthens along the whole protein.
>
> Suppose that the same small molecule docks in more than a single part
> of the multimer, could amber re-score for docking on a part be
> directly compared (energy by energy) with amber re-scoring for another
> part?
>   
I would recommend considering two different binding sites as two
completely different projects.

John
UCSF DOCK Team