Similarity searching application

Batista, J., Tan, L., and Bajorath, J. 2010. Atom-centered interacting fragments and similarity search applications. /. Chem. Inf. Model. 50 79-86. 

Utilization of intelligent systems in chiral chromatography starts with an original project called CHIRULE developed by Stauffer and Dessy [36], who combined similarity searching and an expert system application for CSP prediction. This issue has recently been reconsidered by Bryant and co-workers with the first development of an expert system for the choice of Pirkle-type CSPs [37]. 

A great variety of different methods for multivariate classification (pattern recognition) is available (Table 5.6). The conceptually most simply one is fc-NN classification (Section 5.3.3), which is solely based on the fundamental hypothesis of multivariate data analysis, that the distance between objects is related to the similarity of the objects. fc-NN does not assume any model of the object groups, is nonlinear, applicable to multicategory classification, and mathematically very simple furthermore, the method is very similar to spectral similarity search. On the other hand, an example for a rather sophisticated classification method is the SVM (Section 5.6). 

The standard screening approach when several active molecules have been identified is pharmacophore mapping followed by 3D database searching. This approach assumes that the active molecules have a common mode of action and that features that are common to all of the molecules describe the pharmacophoric pattern responsible for the observed bioactivity. This is a powerful technique but one that may not be applicable to the structurally heterogeneous hits that characterize typical HTS experiments or sets of competitor compounds drawn from the public literature. In such cases, it is appropriate to consider approaches based on 2D similarity searching and we present here a comparison of approaches for combining the structural information that can be gleaned from a small set of reference structures. 

This application of the similar property principle was pioneered by Adamson and Bush (25,26) and has since been very extensively applied. For example, Willett and Winterman used it in one of the first detailed comparisons of measures for similarity searching (27), and it also formed the basis for Brown and... 

The first application of a surface-based pharmacophore correlation vector was reported by Stiefl and Baumann in 2003 [18] with the MaP (mapping property distributions of molecular surfaces) descriptor. They applied their MaP descriptor for QSAR applications. To our knowledge, an application of this descriptor to similarity searching has not been reported. 

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