Heuristics for searching chemical structures

Abstract

Chemical and biochemical structure databases are useful for retrieving information to a wide range of users, ranging from a high school student to a medical research scientist. These databases provide the user with various structure search tools to search and retrive structures and also make relevant structural comparisons. Our database, Klotho, consists of biochemical compounds defined with rules depicting therelations between atoms in the molecules. We have developed methods to recognize a wide variety of structural relationships among molecules. The method exploits these definitions and searches for specific structures in the database using graph similarity algorithms and heuristics about biochemical structure. The heuristics narrow down the search space and speed up the time required to perform the search. Most of the structure search tools implement variations of the popular search methods like substructure search, exact structure search and isomer search. Most existing structure search systems provide options for stereoisomer search in general. And some of these systems allow tautomer search too. Hence we felt the need to develop a tool for specific isomer search. The search methods in this tool are are isomer search, substructure search, and isoconnectivity search. Isomer search matches those compounds which are structural and configurational isomers of the query compounds. Substructure search retrieves those compounds which has the query compound as a part of its structure. Isoconnected structure search retrieves compounds which are identical to the query compound with and without considering stereochemistry. General structure search retrieves chemical property information for compounds. Isoconnectivity structure search retrieves compounds which are identical to the query compound.