The concept of using pairs of atoms and how far apart they are as a way to encode structures underpins many of the grouping techniques that are particularly popular in HTS analysis and other large collections of biochemical data. Here, Carhart, Smith and Venkataraghavan introduce atom pairs and describe how the shortest path between two atoms can be identified by crawling through a molecule starting at each atom in turn to identify the shortest distance to every other atom. This way to encode the structure of molecules is illustrated for acetone and isobutylene and allows for a very compact and general representation that allows connections between molecules to be made that are usefully surprising.
Atom pairs as molecular features in structure-activity studies: definition and applications
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