Similarity Scores

The connection table of the query object (similarity probe) is processed to obtain the set of atom pairs, and then the database file is scanned to evaluate the similarity between the query and each of the database structures. The maximum number of structures that the program will select is specified, as well as the minimum similarity score that a database compoimd must show to be selected. Within these limits, the program will select from the database the structures that are most similar (with the highest similarity value) to the query and will create an output file of compoimd numbers and similarity values, sorted by decreasing similarity, for the selected compounds. 

As an example consider the data presented in Tables 35.1-35.4. These tables are extracted from a much larger data base obtained in an international cooperative study on the sensory aspects of olive oils [1]. Table 35.1 gives the mean scores for 16 samples of olive oil with respect to six appearance attributes given by a Dutch sensory panel. Table 35.2 gives similar scores for the same samples as judged by a... 

Another limitation to the use of PCA comes from the fact that being a linear projection it may introduce mistakes. Indeed, in the projection, data separated in the original space may result in a similar score, a phenomenon like that producing a constellation in the starred sky. 

Finally, the different atoms in each substrate are assigned a similarity score. Because of the computational mechanism, the score is proportional to the exposure of such substrate atoms toward the reactive heme or UDPGA (in CYP or in UGT, respectively) and represents the accessibility component. 

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.

Pharmacophore similarity scoring schemes are represented by the FBPA and ComPharm overlay dissimilarity scores, the expectation being to see low dissimilarity scores matching high activity levels. 

Table 1. Cellulase catatytic domain families, organized by similarity scores as determined successive FastA searches ...

Each of the representative members of a family demonstrated a similarity score of at least 5 standard deviations from the mean score when the search was made using the PIR database, release 24 (28). 

S-score Similarity score based on Tanimoto similarity to selected desirable compounds. 

Basis Product, symmetric similarity score, asymmetric similarity score, lead hopping. 

Fig. 13.3. Comparison of symmetric and asymmetric similarity scores. A virtual product from VRXN-2-00051 is used as a query molecule. The two corresponding Basis Products are VRXN-2-00051 A 1 and VRXN-2-00051 B 1. In reference to the query molecule, their corresponding similarity scores are listed under SS and AS (see equations [1] and...

For every query molecule, LEAP2 is able to return top 10 molecules with best similarity scores ranging from 0.4 for sertraline to 0.9 for celecoxib. Five of 24 searches return PGVL hits 80% or more similar to the query molecules for meaningful follow-up. If the threshold is relaxed to 0.7, then 11 of 24... 

Fig. 13.6. Results from the third validation study. The -axis represents the Tanimoto similarity score of returned hits with respect to their corresponding query molecule, calculated based on the FCFP4 molecular fingerprints (31). The x-axis are drug molecules in Fig. 13.5. Search hits are color coded by the PGVL reactions (VRXN) where they are originated from.

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