Search, similarity

Structure and substructure searching are very powerful ways of accessing a database, but they do assume that the searcher knows precisely the information that is needed, that is, a specific molecule or a specific class of molecules, respectively. The third approach to database searching, similarity searching, is less precise in nature because it searches the database for molecules that are similar to the user s query, without formally defining exactly how the molecules should be related (Fig. 8.3). 

Data storage and querying are the most fundamental requirements of all informatics systems. Thanks to the Oracle Extensibility Framework (a.k.a. Oracle Data Cartridge Technology), chemical structure data can be stored and queried using direct SQL and special query operators, such as substructure search, flexmatch search, similarity search, and formula search. Also, some indexing techniques make these otherwise slow searches fast. Detailed discussions about these databases and cartridges are beyond the scope of this book. Please refer to the vendor s website and product documentation for more information. 

General Methods for Searching Similar Structural Motifs... 

Figure 13.4 Results of a CATS similarity search. Similarity between the query structure (Haloperidol, a D2 antagonist upper left) and database compounds was defined in terms of a topological pharmacophore descriptor. The top 10 most-similar molecules found are shown.

Note that one can consider a quadratic line search similar to one outlined for... 

In addition to binary descriptors, molecular holograms are also useful for similarity searches. Similar to fingerprint, hologram is a vector that contains numerical... 

Searching Similar to the other GWAS, pharmacogenetics-oriented GWAS will... 

Besides similarity searches similarity measures are frequently applied in the analysis and design of combinatorial libraries. ... 

A 2D similarity search is first carried out to find specific fragments in the database (e.g., CC(C==0)N for an amino acid). With the defined pharmacophore patterns, we will search the database using sub-/superstructure search, similarity search, Tanimoto coefficient (146), Tversky search (147), and so on. The search returned hit list will be grouped into a molecular spreadsheet for further studies. The 2D database searches usually are carried out as initial screening, followed by 3D searches. 

An alternative approach to this type of image warping is to develop techniques to identify specific anatomical structures within the tissue (Rasser et al. 2005). These anatomical statistical trained models (STMs) are trained using a large sample of images on which specific features are manually identified. The statistical variability of these features is then calculated and the trained STM can then search similar images to find the best estimation of the structure. 

On the CD-ROM, all the Aijiax values are indexed in the UV Maxima field and can be searched for numerically including range searching. Similarly, the solvent data associated with the UV data are indexed in the UV Solvent field. 

Lazar Lazy Structure-Activity Relationships. Gets the prediction from the toxicity data by searching similar compounds in the database which are associated with a given toxic activity http //in-silico.de/... 

The Statistica program package implements three basic algorithms for CART univariate split, linear combination split, and exhaustive search. Similarly, three stopping options can be chosen prune on misclassificafion error, prune on deviance, and direct stop [11]. 

While we portray the structure of matter in an hierarchical scheme, we also recognise that searching the structures is done at various levels of precision exact match, non-exact match with false positives allowed, non-exact match with false negatives allowed, fuzzy searches, heuristic searches, and similarity searches. Similarity searches themselves can be done at many adjustable levels, and similarity itself is multidimensional. 

The user must be able to store structures in a database and retrieve them. The user must be able to do various structural searching operations, such as exact match, substructure search, similarity search, and formula search. 

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