Similarity searching methods

D similarity search methods are quite well developed. Thus, methods which attempt to find overlapping parts (atoms and functional groups) of the molecular moieties studied were reported first [31]. As discussed above for the case of 2D searching, these methods are of combinatorial complexity. To reduce this complexity some field-based methods have been introduced. In this case, the overlap of the fields of two structures is considered as a similarity measure. 

Sheridan RP, Kearsley SK. Why do we need so many chemical similarity search methods Drug Discov Today 2002 7 903-11. 

Sheridan RP, Kearsley SK. (2002) Why Do We Need So Many Chemical Similarity Search Methods Drug Discov. Today 7 903-911. 

Two recent papers further highlight the difficulty of choosing which similarity searching method to use (29,30). Given the vast array of different molecular descriptors available and the vast number of different similarity measures, this field has been the subject of many publications espousing different methods. As similarity searching and clustering are the easiest, yet very useful,... 

Moffat, K., Gillet, V. J., Whittle, M., Bravi, G., Leach, A. R. (2008) A comparison of field-based similarity searching methods Cat-Shape, FBSS, and ROCS. J Chem Inf Model 48, 719-729. 

Directly related to the similarity-searching methods are cheminformatics methods that try to align the chemical and biological spaces based on mapping procedures. 

Bender, A., Jenkins, J.L., Scheiber, J., Sukuru, S.C.K., Click, M., and Davies, J.W. (2009) How similar are similarity searching methods A principal component analysis of molecular descriptor space. Journal of Chemical Information and Modeling, 49 (1), 108-119. 

Claverie, J. M. (1997b). Exon detection by similarity searches. Methods Mol. Biol. 68, 283— 313. 

The PASTA (Lipman and Pearson, 1985) and Basic Local Alignment Search Tool (BLAST) (Altschul et al, 1990 1997) programs are local similarity search methods that concentrate on finding short identical matches, which may contribute to a total match. 

Part Optical Spectroscopy by S. Thiele and R. Salzer for instance contains the topics basic data treatment, IR- and UV-databases and spectra similarity search methods. Emphasis is given to multivariate calibration mehtods that are now routinely used for quantitative analyses of compounds in complex matrices. Principles of the widely used chemometric methods, such as PCA, PCR, and PLS are explained together with their applications in IR spectroscopy. 

The test set included 400 inhibitors whose ICj values were not known. We first identified 19 scaffolds from Uterature. These have been then searched using similarity search methods (Fig. 3.51). 

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