Substructures Searching Algorithm

There are several basic strategies for the improvement of the performance of substructure search algorithms ... 

The next sections deal exclusively with the second and the third approaches to the optimization of substructure search algorithms. 

A substructure search algorithm is usually the first step in the implementation of other important topological procedures for the analysis of chemical structures such as identification of equivalent atoms, determination of maximal common substructure, ring detection, calculation of topological indices, etc. 

Chen, L., Nourse, J. G., Christie, B. D., Leland, B. A., and Grier, D. L. (2002) Over 20 years of reaction access systems from MDL a novel reaction substructure search algorithm. J. Chem. Inf. Comput. Sci. 42, 1296-1310. 

Another crucial aspect of the validation process is the test of how well described and represented the molecule is in the map of the chemical toxicity space that the regression equation represents. If the substructural key does not exist in the database used to build the model, then it is unlikely that the compound can be accurately estimated. In addition, if compounds similar to the test compound do not exist, then a comparison as was done above cannot be conducted and a measure of the performance of the model with compounds similar to the test material cannot be made. This type of validation requires a large database and a substructural search algorithm, and should be included in a QSAR estimate. 

In order to find the correct rate estimation parameters for a bimolecular reaction, one must first find the best-match functional group A in one reactant, using a substructure search algorithm very similar to that used to find thermochemical group values. Then one must find the best-match functional group B in the second reactant in a similar way. Then one can look up the rate estimation parameters for this reaction type using A and B as the keys. 

Early Work in the Development of Maximal Common Substructure Search Algorithms... 

Downs GM, Lynch MF, Willett P, Manson GA, Wilson GA. Transputer implementations of chemical substructure searching algorithms. Tetrahedron Comput Methodol 1988 1 207-217. 

Wipke and Rogers have also simulated the operation of a parallel substructure search algorithm on a conventional computer. Their approach uses parallelism to get round the problems of the brute force approach, but it has not so far been tried on a real parallel machine. 

Downs, G.M. Lynch, M.F. Willett, P. Manson, G.A. Wilson, G.A. Transputer Implementation of Chemical Substructure Searching Algorithms . Tetrahedron Comput Methodol 1988,1(3), 207-217. 

Five main strategies have been used, often in combination, to improve the performance of substructure searching algorithms ... 

---