Daylight similarity

DayCart is a software cartridge which offers a range of operation on an Oracle database, such as complete structure, similarity, and substructure search. The software can be obtained from Daylight Chemical Information Systems, Inc. (Mission Viejo CA) URL www.daylight.com... 

Bradshaw J 1997. Introduction to Tversky Similarity Measure. At http //www.daylight.com meetings / mu g97 / Bradshaw / MUG97 / tv tversky.html. 

The pragmatic beauty of the chemical fingerprint is that the more common features of two molecules that there are, the more common bits are set. The mathematic approach used to translate the fingerprint comparison data into a measure of similarity tunes the molecular comparison [5]. The Tanimoto similarity index works well when a relatively sparse fingerprint is used and when the molecules to be compared are broadly comparable in size and complexity [5]. If the nature of the molecules or the comparison desired is not adequately met by the Tanimoto index, multiple other indices are available to the researcher. For example, the Daylight software offers the user over ten similarity metrics, and the Pipeline Pilot as distributed offers at least three. Some of these metrics (e.g., Tversky, Cosine) offer better behavior if the query molecule is significantly smaller than the molecule compared to it. 

Apply separately to the plate 5 pL of each solution. Develop over a path of 15 cm using a mixture of 20 volumes of ammonium acetate solution R, 40 volumes of dioxan R and 40 volumes of methanol R. Dry the plate in a current of warm air for 15 min and expose it to iodine vapor until the spots appear. Examine in daylight. The principal spot in the chromatogram obtained with the test solution is similar in position, color, and size to the principal spot in the chromatogram obtained with reference solution (a). The test is not valid unless the chromatogram obtained with reference solution (b) shows two clearly separated spots. 

To demonstrate this, Figure 2.8 shows the comparison of similarity for Daylight structural and biological fingerprints created from a panel of 154 assays from the BioPrint database (measured by pairwise Tanimoto distance for 347 drugs with MW 200-600 60031 points) [6]. Figure 2.8a shows the overall scatter plot of the... 

Fig. 18.8 Similarity profile for filtered set of commercially available compounds. 5000 randomly selected compounds from the Available Chemicals Directory that pass the REOS filter were ranked according to their Tanimoto similarity scores (vertical axis) using Daylight fingerprints. 2886 compounds (58%) had similarity scores below 0.85.

One or more lead molecules may be used as a focusing target. Similarity metrics include Daylight fingerprint Tanimoto similarity. The penalty score for each compound in the library is defined as the distance between it and the most similar lead molecule. The penalty score for the library is the average of the individual compound penalty scores. QSAR predictions and docking scores can also be used in this term. 

Figure 2. The color-rendering index (CRI), of similarity to daylight-rendering, dependence upon choice of triad of spectral lights to form white light of daylight-color. Wavelengths of two components are fixed at their peaks, and the wavelength of the third component is varied. Optimum combination appears in Figure 3.

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