How I'll know whether the protein and the ligand are binding strongly from the docking score? Is there anything like a minimum/maximum docking score which I should get to confirm the strong interaction between the ligand and protein? I would like to extend my work to wet lab based on the docking result.
Beware of using docking scores as a surrogate for binding affinity. Docking scores are generally bad at telling which binding conformations are useful, they only optimize a small molecule inside a binding pocket. It is generally better, if you know about the protein and its ligands in vivo, to check X (lets say 100) of the best scoring poses and decide by visual inspection if they make sense or not. For those that make sense you can estimate if it would be a good binder and pursue it further. Sorry this is probably not the answer you wanted, but making decisions on the docking score alone would be a mistake in my opinion.
Antonio has right.
In general docking scores are very arbitral thus they can be used only as a some kind of measure, which in most cases are only a hint.
If you can't believe simply perform an experiment - perform docking for a set of systems with known, i.e., IC50.
Docking is only finding some positions, that's all.
This is true that docking score is not completely reliable measure. Actually there is no such minimum or maximum criteria in considering docking score. Docking score will not give answer for affinity. Docking score can be compare with existing co-crystallized molecule after protein validation and can be checked for interactions and active site binding. After the docking as a preliminary bases you can do MM-GBSA and LIAISON in SCHRODINGER to have an idea for binding energy.
Every one suggestions are nice, but none of you addressed the question. After 3 years since the question posted, even am searching answer for the similar question. It would be great if some one give exact answer to the question.
As i know best pose found so far has a score of -60.0 kcal/mol, poses with a score more positive than 40.0 kcal/mol are rejected.
OK thanks. I have similar question as well thanks agaian for conformation
Glide score should never be used to select the strong binders, but it may be used to eliminate the really bad ones. Usually the really bad binding poses (i.e. partly exposed to water, bad fitting in the cavity or unsatisfied contacts) correlate with poor glide scores in my experience. So, a very relaxed cutoff of glide score can be used to eliminate the really bad poses, followed by a more accurate method such as FEP or mmgbsa to select the top binders. I normally use a maximum glide score cutoff of zero or -2 to retain the initial poses before commencing further processing. Not claiming that this choice is the best though.
Supriyo Bhattacharya
Hypothetically, Does a score of Zero mean that the ligand has no active interaction with the receptor? hypothetically that is.
Is binding energy of 9 kcal/mol (Gibbs' free energy) not considered as threshold or critical? Is lesser the number of conformations (folding) the better, as more folding means more energy expenditure, lower stability?
i wonder if docking gives 4 possible posses at around - 8 kcal/mol each, is this a good indicator of strong interactions?
the docking score give an idea about binding, but should combined with visual inspection of the poses attained from docking, it also depend on what software used, for schrodinger there is a docking score and glide docking which is 2 different parameters, also you shoul look for emodel, einternal enegery, somtimes the score cannot cover everything.
i hop this will help.
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