Substructure matching

Each molecular transformation applied by Leatherface is specified by a SMARTS definition followed by a series of instructions that specify how the substructure matched by the SMARTS is to be modified. The first example shows how neutral carboxylic acids are converted to their more physiologically relevant anionic forms. The Pit instruction indicates that a single proton is to be removed (—1) from the atom matching the third atom in the SMARTS. 

The database search process starts with a rapid screening process within which molecules possessing properties required from potential hits are sorted out from those that can be excluded a priori. The screen involves substructure match followed by screens matching three-dimensional pharmacophore features, molecular shapes or exclusion volumes and text constraints (ID properties) if present in the query (through Oracle). All this greatly reduces the number of potential hit compounds in the database. The next step of the search pro-... 

Xu, J. (1996) GMA a generic match algorithm for structural homomorphism, isomorphism, and maximal common substructure match and its applications./. Ghem. Inf. Gomput. Sci, 36, 25-34. 

Every structure containing phenol as a substructure must have a molecular formula with 6 or more C atoms and 1 or more O atoms. Structures with fewer C or O atoms can be immediately ruled out as possible matches for phenol. Of the remaining structures, there will be some that satisfy the molecular formula comparison yet do not match phenol. The more time-consuming matches function will be used only for the final determination. Overall, the process of finding substructure matches will be faster. Exactly how much faster depends on the number of rows that can be quickly ruled out using the faster molecular formula comparison. It also depends, of course, on how fast the molecular formula comparison can be done. 

The previous section shows how molecular structures stored in an RDBMS can be made available to client programs that traditionally read molecular structure files. The advantage of storing molecular structures in an RDBMS is that the information can be used from within the database, as well as by external clients. For example, it would be possible to search a table of molecular structures for three-dimensional overlap, much like it might be searched for substructure match. Of course, such search functions need to be written and installed as extensions to an RDBMS, just like the matches functions was done for substructure searches. This section shows some possible ways this might be accomplished. 

Partitioning-Relaxation-Based Substructure Matching Algorithms... 

Substructure Matching Techniques for Searching Large Databases... 

All of the substructure match algorithms described so far rely entirely on the topology of 2-D molecular structures. These algorithms can be further extended to compare query-target pairs of structures containing stereochemistry [42]. It is in this area where atom coordinates of 2-D structures play a certain role The configuration of double bonds and tetrahedral centers can be computed from atom display coordinates and bond symbols [42],... 

Substructure Match on all components Formula Search on all components Tautomer Search on all components... 

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