STABILITY IN MOLECULAR FINGERPRINT COMPARISON
Anthony O. Nicholls, Brian Kelley · 2013
The comparison of molecular structures by what are called 2D representations, or fingerprints, is one of the more widely used and useful of techniques from cheminformatics. However, agreement between calculated similarity and chemical intuition is by no means certain. In fact, methods can sometimes claim molecule A is similar to B, and yet a slight change to molecule B can completely destroy this correspondence, that is, measurements are sensitive or fragile. Alternatively, two molecules that appear very different to the eye can sometimes be reported as apparently similar. Here, we investigate these phenomena, their practical consequences, and how they point toward the potential for more useful methods of molecular comparison, such as edit distances or specifically weighted fingerprints.