In the fields of computational chemistry and molecular modelling, scoring functions are fast approximate mathematical methods used to predict the strength of the non-covalent interaction (also referred to as binding affinity) between two molecules after they have been docked. Scoring functions have also been developed to predict the strength of other types of intermolecular interactions, for example between two proteins or between protein and DNA. What is the best scoring functions for docking? How can I select the best scoring functions for docking?
There is nothing like that becze each scoring function has it's own benefit and drawbacks based on parameters involve . So you can't determine which one you need to use before trying to asses it's validity with your docking or based on previous publications .
All of the answers provided so far are correct, there is no best scoring function for all possible cases. Different functions perform better in different cases, heres two possible cases a deeply buried hydrophobic pocket, versus a shallow groove site with lots of solvent accessibility a given function may do well in the first case and absolutely fail in the second. The best method is to test a variety on binding sites similar to what your interested in and if possible ligands similar to yours, at the bare minimum try some redocking runs using different scoring functions.
The best scoring function does not exist yet. What you can do is to make an external one yourself for the target you choose. For istance by making a 3-D QSAR model on docked structures or co-crystallized ligand.
Docking and subsequent MD on docked complexes can give the suitability of scoring function used in docking program.
A general statement cannot be made. Even though, it can be said that scoring function with explicit solvation/desolvation penalties, charge tretment and buried hydrophobic paches terms; other than the normal interaction terms would outperforms in most instances.
However, it becomes a trend to use score normalization strategy and the same has been asked in most standard journal.
Article The scoring bias in reverse docking and the score normalizat...
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