Virtual false negative

Finally we hope to see that more validation studies are conducted to compare any new search method with the reference exhaustive search (of course on a smaller validation virtual space of 104-106). Only through this type of rigorous validation studies, one can truly probe the rates of false positives and false negatives as well as the fold increase in search speed. This in turn allows end users to make informed decisions on which search method will be a best match for their specific tasks. 

Equation (3), which is an application of Bayes theorem, is referred to as the Positive Predictive Value. The parameter p is unknown but believed to be very small (<0.01) for large virtual libraries. 1 - p is the power (or 1 - type II error, where ft is the false negative error rate) and a is the type I error, also called the size of a test in the hypothesis testing context, or the false positive error rate. The last equation defines the probability that a molecule is determined to be a hit in a biochemical assay given that the virtual screen predicts the molecule to be a hit. This probability is of great interest because it is valuable to have an estimate of the hit rate one can expect for a subset of molecules that are selected by a virtual screen. 

Mass spectrometry (MS) is highly selective. The ability to further perform tandem mass spectrometry (MS/MS) analysis when a compound is detected to confirm the detection virtually eliminates false positive and negative alarms. But MS/MS analysis must be completely automated for the average GI to be able to perform it. A clever hand-held chemical and biological mass spectrometer has been developed that weighs only 4.3 pounds. The problem with the unit is production of the necessary vacuum, which requires 35 amps at 24 volts. Thus, battery-operated portable mass spectrometry is not yet available. 

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