Similarity searching recall

Table 3 Recall at 5% achieved by Conventional, Single-molecule Similarity Searching...

Figure 1. Comparison of the average recall at 5% obtained with group fusion (GF) and similarity searching (SS) using the ECFP 4 descriptors and 30 MDDR activity classes chosen as being of low, medium and high diversity. The upper part of the figure shows the recall at 5% obtained with GF vs. recall at 5% obtained with SS, while the lower part shows the diversity (as measured by the mean pair-wise similarity) vs. the ratio of the recalls at 5% obtained with GF and with SS.

Table 6 Mean recall at 5°/o for Conventional Similarity Searching (SS) with just a Single Reference Structure and Turbo Similarity Searching (TSS) using different numbers of NNs...

Table 8 Mean Recalls at 5% for Similarity Searching (SS), Conventional Turbo Similarity Searching using Croup Fusion (TSS-CF) and Turbo Similarity Searching using Substructural Analysis (TSS-SSA) and Binary Kernel Discrimination (TSS-BKD)...

The relationship between IR and chemical similarity searching is discussed in detail by Edgar et al. (11) who summarize the various effectiveness measures in terms of the 2 x 2 contingency table shown in Table 1. In this table, it is assumed that a search has been carried out resulting in the retrieval of the n nearest neighbors at the top of the ranked output. Assume that these n nearest neighbors include a of the A active molecules in the complete database, which contains a total of N molecules. Then the recall, R, is defined to be the fraction of the active molecules that are retrieved, i.e.,... 

It is inconvenient to have to specify two measures, i.e., recall and precision, to quantify the effectiveness of a search. The Merck group have made extensive use of the enrichment factor, i.e., the number of actives retrieved relative to the number that would have been retrieved if compounds had been picked from the database at random (12). Thus, using the notation of Table 1, the enrichment factor at some point, n, in the ranking resulting from a similarity search is given by... 

To sum up, the choice of operating conditions for a specific FFF application is made in a way that recalls the general criteria used in chromatography. An accurate search of literature addressed to similar samples that have been already analyzed by FFF techniques is very useful. A number of specific reviews have been published concerning, for example, enviromnental, pharmaceutical, and biological samples (see Section 12.5). As previously mentioned above, one of the most important factors is the stability of the considered colloidal system, for which a great deal of information can be obtained from specialized literature, such as colloid, polymer, and latex handbooks [33], For example, the use of the proper surfactant (e.g., Fl-70) is common for SdFFF applications. Polymer analysis with ThFFF requires solvent types similar to those employed in size exclusion chromatography. 

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