What score value is considered acceptable when using Vina Autodock tool for molecular docking simulations?


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The answer is "Depends". But the best thing is always to look at what you ended up with and do some triaging before buying/synthesising anything. By triaging I mean filtering by its properties (.e.g. Lipinski, reactivity, synthetic feasibility etc. —discussed in this Bioinfo SE question).


Regardless of docking software used, a forcefield free-energy score is a result of the scoring function used and of the properties of the molecule —including VENA which uses a hybrid score function.

This score is not, but generally is set up to try to match, the actual phys-chem one. Gibbs free energy is measured in kcal/mol (or less commonly in kJ/mol). A hydrogen bond is about 2 kcal/mol, a π-π bond 1 kcal/mol and a salt bridge 3. The average energy of a collision of RT water molecules is 0.6 kcal/mol.

Therefore, if you dock multiple compounds (virtual library screen, VLS) you sort by free energy to see the strongest binders and consider the top ones. However, a catch is that this will be biased by MW.

Also, it is useful to score the hits with a different program (say Gold or ICM-dock).

Ligand Efficiency

A variant metric that is employed when your hits vary in size and when they are over a given size (e.g. not fragments under 200 Da) is Ligand Efficiency (LE), which is the ratio of your score over the number of heavy atoms (ref).

Single compound

If you have a single compound and want to know if it binds acceptably, then this is a length-of-a-piece-of-string question as every compound has an affinity constant to a given protein, except most may be beyond their solubility. Initial hits will have µM affinity, while a lead will have nM affinity. However, a KD is not a ∆G and depends on your protein.


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