Abstract
A novel chemical ontology based on chemical functional groups automatically, objectively assigned by a computer program, was developed to categorize small molecules. It has been applied to PubChem and the small molecule interaction database to demonstrate its utility as a basic pharmacophore search system. Molecules can be compared using a semantic similarity score based on functional group assignments rather than 3D shape, which succeeds in identifying small molecules known to bind a common binding site. This ontology will serve as a powerful tool for searching chemical databases and identifying key functional groups responsible for biological activities.
Original language | English |
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Pages (from-to) | 4685-4691 |
Journal | Febs Letters |
Volume | 579 |
Issue number | 21 |
DOIs | |
Publication status | Published - 29 Aug 2005 |
Externally published | Yes |
Keywords
- ontology
- small molecule
- functional group
- pharmacophore
- semantic similarity