Search compounds

Trivial or trade namc.s can be stored and searched as character strings. Their use is the simplest and most intuitive way of storing chemical information. However, being not subject to strict rules, their formation does not reflect accurately the molecular composition. Hence, the structure of the searched compound cannot be derived from them. Thus, a name such as "Flexricin does not tell the user very much. Furthermore, many more than one trivial or trade name for a given compound usually exist. 

Fig. 6.6 Rules for extracting essential parts and making queries for searching compound databases. 1 An example of output structures...

An expansion of structural similarity searching to allow search by chemical substructures in also available as a feature of the Search Compound By Structure function (Advanced Search) of... 

MetaDrug. In this case a structure file or sketched structure (see Note 3) is treated as a component substructure and all compounds containing this structure are returned by the search. To search compounds by substructure ... 

With today s computational resources it is usually not a problem to exhaustively search compounds from corporate collections, vendor libraries, or small combinatorial libraries, which typically range in the order of 10 -10 molecules. However, for large virtual combinatorial libraries and collections thereof it becomes quickly unfeasible to enumerate all possible virtual molecules in advance due to combinatorial explosion. Consequently, there has been an increasing interest in computational methods to find alternative ways to systematically search large virtual combinatorial libraries, allowing a dramatic expansion of unexplored chemical space. 

For example, suppose that an HTS assay results in a number of actives. A similarity search is then conducted on the actives and based on the search compounds are submitted to an HTS re-screen. Frequently compounds were found to be active in the re-screen that were inactive in the original HTS assay. The likely reason is the kinetic phenomenon of compound precipitation from medium time length storage of DMSO master plates. Active compounds were not detected in the primary screen because these compounds were not available to the primary screen. They precipitated from the stored master DMSO plates. The re-screen is performed with freshly DMSO solubilized samples (within the one working-day window) allowing a better detection of a truly active compound. 

Shimura, M., Zhou, Y., Yoshikawa, T. et al. (1999). Inhibition of Vpr-induced cell cycle abnormality by quercetin a novel strategy for searching compounds targeting Vpr. Biochemical and Biophysical Research Communications, 261, 308-316. 

Within the document not all text notes have to be in line with the searched compound. The document is written to the answer set as soon as one structure... 

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