Substructure matching techniques

Substructure Matching Techniques for Searching Large Databases... 

Database searches can be used to find a reference to a known compound with a matching substructure. This is a particularly good technique if a portion of the molecule has an unusual structure. It may indicate a synthesis route or simply identify a likely starting material. 

The various match factors calculated by the matching program are listed in Table I. The overall match factor (PT) is a combination of forward and reverse searching techniques. It takes into account the deviations in intensity of the sample spectrum peaks with respect to the candidate spectrum peaks and vice versa for all peaks in both spectra. The pattern correspondence match factor (PC) is a forward searching match factor which takes into account the intensity deviations of sample spectrum peaks with respect to the candidate spectrum peaks for peaks common to both spectra. This factor detects structural similarities, such as substructures, based on common spectral patterns. NC, NS, and NR give an indication of the number of peaks upon which the match was based and in which direction it was most successful. IS and IR indicate the magnitude of the ion current unmatched in each direction. These match factors are similar to those proposed by Damen, Henneberg, and Wiemann (9). 

Willett and co-workers ° have developed several novel and useful techniques in molecular similarity based on substructural fragments. These approaches are based on the frequency of occurrence of generated fragment descriptors within the molecular graph. Success of these methods has been shown in 2D and 3D matchings of chemical structure, classification of chemical data bases, as well as property estimation. 

A substructure technique is used in the model for which the whole calculation domain is divided in several small domains. The matrix equations are generated in each subdomain. The solutions in each subdomain are solved separately based on their own boundary values. The solution for the entire domain is obtained by matching the results at the imaginary boundaries between those subdomains. This technique largely decreases the matrix size, thus effectively accelerating the calculation. 

The described procedure for connecting different substructures implies that the finite element mesh at the interface of the substructures is identical. However, there are more advanced techniques which allow the connection of substructures even when neither mesh pattern nor element types match along the interface (Knight et aL 1991 Zhao et al. 1999 Dohrmann et al. 2000 Gmiir and Kauten 1993). 

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