title: 2D depiction of fragment hierarchies.
abstract: Drug discovery projects often involve organizing compounds in the form of a hierarchical tree, where each node is a substructure fragment shared by all of its descendent nodes. A method is described for producing 2D depiction layout coordinates for each of the nodes in such a tree, ensuring that common fragments within molecular structures are drawn in an identical way, and arranged with a consistent orientation. This is achieved by first deriving a common numbering scheme for common fragments, then using this scheme to redepict each of the molecules, one fragment at a time, so that common fragments have common depiction motifs. Once complete, the distinct root branches can be overlaid onto each other, after which all of the fragments and whole molecules have a common layout and orientation. Several methods are described for preparing visual representations of molecular structure hierarchies alongside activity information. Combining high level tree display and structure depiction showing common features readily facilitates insight into structure-activity relationships.
authors.affiliation: Chemical Computing Group, Inc., 1010 Sherbrooke Street West, Suite 910, Montreal, Quebec H3A2R7, Canada. aclark@chemcomp.com
authors.forename: Alex M
authors.initials: AM
authors.lastname: Clark
mesh_terms: D000465:Algorithms; D051546:Cyclooxygenase 2 / Q000378:metabolism; D052246:Cyclooxygenase 2 Inhibitors / Q000737:chemistry / Q000494:pharmacology; D003626:Data Display; D055808:Drug Discovery / Q000379:methods*; D005493:Folic Acid Antagonists / Q000737:chemistry / Q000494:pharmacology; D015203:Reproducibility of Results; D013329:Structure-Activity Relationship; D013762:Tetrahydrofolate Dehydrogenase / Q000378:metabolism
chemical_list: D052246:Cyclooxygenase 2 Inhibitors; D005493:Folic Acid Antagonists; D051546:Cyclooxygenase 2; D013762:Tetrahydrofolate Dehydrogenase