4.4. Pairs

ADMET Predictor uses the term “molecular pair” in a manner similar to the term “activity cliff”, the latter generally referring to a pair of molecules having similar structures but significantly different values of activity (Maggiora 2006). Occurrences of activity cliffs are important to synthetic chemists, as they indicate which small changes in molecular structure produce large changes in biological action, thus providing insights into which portions of a molecule should, or should not be modified.

ADMET Predictor’s matched molecular pairs (MMP) are a generalization of the activity cliff concept to include any property, whether it be activity, toxicity or any other measured or calculated value of the molecules. In fact, ADMET Predictor even supports the concept of no selected property, in which case the MMP method is simply a way of identifying pairs of molecules having similar structure.

There are a number of different ways to generate pairs, each of which is briefly discussed in this section. The first choice that must be made is whether to identify all of the pairs that exist within a given set of molecules, or to identify only those pairs that include a particular molecule of interest. The latter is obviously a much simpler and faster operation, and so should be chosen whenever a single reference structure can be easily identified.

Pairs can be generated using CHEMISTRY>>Generate Pairs (Activity Cliffs) or by clicking on the corresponding toolbar button

This will display the Generate Pairs dialog, which is described in the Pair Generation Options section. Once pairs have been generated, they can be visualized using the Pairs tab.

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