Chemical databases searching

Web-based chemistry is a reality. With MDL s Chemscape Server and Chime Pro family of products, scientists can read interactive chemistry documents, perform chemical database searches, and reach out to the wealth of chemical and biological information available on the Web. First introduced in 1997, the Chemscape and Chime Pro solutions have become industry standards for communicating chemical information on the Web and for accessing, searching, and visualizing "live" chemical structures within Web environments. 

Molecular Gngerprints are string representations of chemical structures designed to enhance the efficiency of chemical database searching and analysis. They can encode... 

Nowadays, Markush structures are utilixed mainly in patent databases, where they describe a number of different chemical compounds. Searching in patent databases is very important for companies to ascertain whether a new compound is... 

The initial step is to identify which database, from a few thousands worldwide (about 10 000 in 2002), provides the requested information. The next step is to determine which subsection of the topic is of interest, and to identify typical search terms or keywords (synonyms, homonyms, different languages, or abbreviations) (Table 5-1). During the search in a database, this strategy is then executed (money is charged for spending time on some chemical databases). The resulting hits may be further refined by combining keywords or database fields, respectively, with Boolean operators (Table 5-2). The final results should be saved in electronic or printed form. 

Thus, if the user wants to look for literature including requested chemicals or reactions, it is possible to query the database by the first option Chemical Substance or Reaction , The compound can be entered as a query in three different ways drawing the chemical structure in a molecule editor (Chemical Structure) searching by names or identification number, such as the CAS Number (Structure Identifier) and searching by molecular formula (Figure 5-12). 

Large chemical databases, combinatorial libraries, and data warehouses have become indispensable tools in modem chemical research. Accordingly, stmctural information must be stored in these databases and searched in an appropriate manner. 

A useful empirical method for the prediction of chemical shifts and coupling constants relies on the information contained in databases of structures with the corresponding NMR data. Large databases with hundred-thousands of chemical shifts are commercially available and are linked to predictive systems, which basically rely on database searching [35], Protons are internally represented by their structural environments, usually their HOSE codes [9]. When a query structure is submitted, a search is performed to find the protons belonging to similar (overlapping) substructures. These are the protons with the same HOSE codes as the protons in the query molecule. The prediction of the chemical shift is calculated as the average chemical shift of the retrieved protons. 

Correlations between structure and mass spectra were established on the basis of multivariate analysis of the spectra, database searching, or the development of knowledge-based systems, some including explicit management of chemical reactions. 

Computer Representations of Molecules, Chemical Databases and 2D Substructure Searching... 

Structure and Nomenclature Search System. This system links the collection of chemical databases found in the Chemical Information System (CIS), one of the first interactive systems for stmcture and substmcture searching. References from the separate files can be retrieved by SANSS using CAS Registry Numbers, and the database of stmctures may be searched for stmctures or substmctures. An adaptation of the SANSS software for substmcture searching has been incorporated in the Dmg Information System of the National Cancer Institute for its own use (54). 

The following chemical databases are available for searching in MACCS-II. ChemicalDirectoy Database contains a combined catalogue of 66 commercial suppHers of more than 77,000 organic chemicals. AL4.CCS-II Drug Data eport based on the Prous Dmg Data Report, includes 39,000 compounds with information on therapeutic indication, biological action, phase of development, related patents, and Hterature references. MUSE Database the tutorial database for MACCS-II, contains over 100 compounds. 

Chemically related database searches can be used to estabhsh concepts and patentable ideas. For instance, searches have identified researchers using particular monomers in a potentially patentable latex formulation found precedents for a polymeric emulsifier summarized pubHcations of people being considered as consultants, expert witnesses, employees or speakers to an industrial group and provided market description information for a new pigment manufacturing firm to identify target markets. 

Subject Categories. The deterrninant for user selection of a database is usually subject matter. That is, when chemical information is desired, a chemical database is selected. The form or media of the database is of secondary importance. The type of search may dictate the need for a full-text or statistical database. If none exists, however, a bibhographic database in the topic area may be used to locate full-text or numeric compilations in hard-copy form. 

This review includes most of the published articles from the defined area and excludes only imidazoquinolines, which were reviewed in Weissberger-Taylor s series The Chemistry of Heterocyclic Compounds (81MI1). Comprehensive Heterocyclic Chemistry II (96MI1) mentioned only some of the azoloquinolines in the first edition the authors omitted citations about this type of compounds. The trend toward interest in these compounds can be illustrated by the number of citations in Chemical Abstract as shown in Table I. Besides Chemical Abstracts Substance/Subject (Collective) Indexes, the MDL database search has been used. 

In this chapter, we will discuss the present status of CHIRBASE and describe the various ways in which two (2D) or three-dimensional (3D) chemical structure queries can be built and submitted to the searching system. In particular, the ability of this information system to locate and display neighboring compounds in which specified molecular fragments or partial structures are attached is one of the most important features because this is precisely the type of query that chemists are inclined to express and interpret the answers. Another aspect of the project has been concerned with the interdisciplinary use of CHIRBASE. We have attempted to produce a series of interactive tools that are designed to help the specialists or novices from different fields who have no particular expertise in chiral chromatography or in searching a chemical database. 

In fact, when chemical class searches are chosen, the user should change as many of the "U" designations in Chemical Attributes as possible. When a U" is left, the system assigns a "worst case" value to that attribute in order to make the most conservative choice of materials. Thus, if the answer to the question, "Is the chemical a known or potential carcinogen " is "U," the system assigns it a "yes" because that is the worst case and will produce the most conservative selections when the database is evaluated for materials that have been tested against the class of compounds under consideration. 

The previous sections have summarized the basic techniques available for searching chemical databases for specific types of query. Another important database application is compound selection, the ability to select a subset of a database for submission to a biological testing program. The selection procedure can be applied to in-house databases, to externally available compound collections, or to virtual libraries, that is, sets of compounds that could potentially be synthesized. 

Web in the life of the medicinal chemist. One may see the development of alerting services for the primary medicinal chemistry journals. The Web-based information search process could be replaced by a much more structured one based on metadata, derived by automated processing of the original full-text article. To discover new and potentially interesting articles, the user subscribes to the RSS feeds of relevant publishers and can simply search the latest items that appear automatically for keywords of interest. The article download is still necessary, but it may be possible for the client software to automatically invoke bibliographic tools to store the found references. Another application of the Chemical Semantic Web may be as alerting services for new additions to chemical databases where users get alerts for the new additions of structures or reactions. 

The internet allows the linking of computers which are tuned for database searching (and which may access a world wide database of information, which is not limited by the published literature but also includes research results which are available only on the internet) with computers which are capable of calculating chemical reactivity. It is now easy for me, for example, to do different sorts of literature searches on computers in Bath, Daresbury, and in Manchester, and to analyse the data using computers in Cambridge, all without leaving my office. 

The E-state indices may define chemical spaces that are relevant in similarity/ diversity search in chemical databases. This similarity search is based on atom-type E-state indices computed for the query molecule [55]. Each E-state index is converted to a z score, Z =(% -p )/0 , where is the ith E-state atomic index, p is its mean and O is its standard deviation in the entire database. The similarity was computed with the EucHdean distance and with the cosine index and the database used was the Pomona MedChem database, which contains 21000 chemicals. Tests performed for the antiinflamatory drug prednisone and the antimalarial dmg mefloquine as query molecules demonstrated that the chemicals space defined by E-state indices is efficient in identifying similar compounds from drug and drug-tike databases. 

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