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[mtim]

If I have two separate crystal structures:
a) co-crystal of a protein with a ligand;

 crystal of a protein alone
What can I study using information from “a)” : docking accuracy, best binding pose/highly ranked binding pose?
What can I study using information from “b”: comparing changes in binding site conformations? What metrics describes these changes?

 

regards, m

[Wendt]

These are pretty basic questions on docking:

 re a) you can use co-crystal structures to re-dock the bound ligand and measure how close the docked pose fits the experimental pose, i.e. in terms of rmsd.

re you can compare the protein part of the co-crystal with the protein alone to identify potential movements of sidechains or backbone upon ligand binding, i.e. examine the extent of induced fit. 

 

I am not sure what you want to achieve. Can you please put your questions into perspective.

 

Best,

 

Bernd