Fragment-based similarity searching

Chen, X., Reynolds, . H. (2002) Performance of similarity measures in 2D fragment-based similarity searching comparison of... 

After the fragment search is conducted for the chloro aromatic fragment, a similar search is performed on the fragment centered about atom 2, which contains a bromo substituent. This fragment probe (FPROBE) search, shown in Figure 13, results in 229 occurrences of this fragment in compounds in the NIOSH RTECS data base. 

Figure 8.3 Example of a 2D similarity search, showing a query molecule and five of its nearest neighbors. The similarity measure for the search is based on 2D fragment bit-strings and the Tanimoto coefficient.

Many different structural descriptors have been developed for similarity searching in chemical databases [4] including 2D fragment based descriptors, 3D descriptors, and descriptors that are based on the physical properties of molecules. More recently, attention has focused on diversity studies and many of the descriptors applied in similarity searching are now being applied in diversity studies. Structural descriptors are basically numerical representations of structures that allow pairwise (dis)similarities between structures to be measured through the use of similarity coefficients. Many diversity metrics have been devised that are based on calculating structural (dis)similarities, some of these are described below. 

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