The aim of virtual screening is to identify molecules of novel chemical structure that bind to the macromolecular target of interest. Thus, success of a virtual screen is defined in terms of finding interesting new scaffolds rather than the total number of hits. Interpretations of virtual screening accuracy should, therefore, be considered with caution. Low hit rates of interesting scaffolds are clearly preferable over high hit rates of already known scaffolds.
Most tests of virtual screening studies in the literature are retrospective. In these studies, the performance of a VS technique is measured by its ability to retrieve a small set of previously known molecules with affinity to the target of interest (active molecules or just actives) from a library containing a much higher proportion of assumed inactives or decoys. There are several distinct ways to select decoys by matching the properties of the corresponding active molecule and more recently decoys are also selected in a property-unmatched manner. The actual impact of decoy selection, either for training or testing purposes, has also been discussed.
By contrast, in prospective applications of virtual screening, the resulting hits are subjected to experimental confirmation (e.g., IC measurements). There is consensus that retrospective benchmarks are not good predictors of prospective performance and consequently only prospective studies constitute conclusive proof of the suitability of a technique for a particular target.