Hello, pysicochemists:
could you please advise how to calculate docking accuracy? What is a mathematical equation? What are existing programs for this or shall I write a script? (also what is the difference between docking accuracy and docking performance)
regards, M
Docking accuracy measures how accurately you can predict the reality, i.e. how well you can reproduce experimental structures. The most widely used way to quantify docking accuracy is to use rmsd values of atom centers between the docked pose and the crystallographic one. You don’t need a script when you use the program Surflex-Dock as this will be part of the output. Please refer to the Surflex-Dock manual for specific command line options.
Docking performance aims to compare different docking protocols or different docking software, i.e. how well the docking is done. For docking performance you can use docking accuracy as a measure, but in most cases enrichment studies are used where you dock structures from a mixed pool of active and inactive structures and enrichment can be achieved when the binding scores for the active structures are higher than for the inactive ones.
Hope, this helps.
Bernd
Hello Bernd, I appreciate your response, thanks.
What is the optimal protocol for preparing the receptor for docking:
shall I leave H2O or shall I remove H2O just from the binding site or from all the protein?
If I have two separate crystal structures:
a) cocrystal of a protein with a ligand;
b) 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 “b”?
regards, m