Feature Trees: A new molecular similarity measure based on tree matching

between small organic compounds. Instead of a linear representation like
fingerprints, a more complex description, a {\em feature tree}, is
calculated for a molecule. A feature tree represents hydrophobic fragments
and functional groups of the molecule and the way these groups are linked
together. Each node in the tree is labeled with a set of features representing
chemical properties of the part of the molecule corresponding to the node. The
comparison of feature trees is based on matching subtrees of two feature
trees onto each other. Two algorithms for tackling the matching problem
are described and results achieved on two data sets are presented.