Chemical Substructure

Chemical Substructure Databases. Several patent databases are searchable by chemical substmcture (99). These are designed to give higher relevance of retrieval when searching chemical compounds than the bibHographic or full-text databases. 

As a first conclusion, this work shows that similarity coefficients, which code molecules in terms of chemical substructures, are useful to assess the efficiency of CSPs. The purpose of this work was not to propose a new method for solving the... 

Recognition of Chemical Substructures from Mass Spectra... 

In this example, we apply D-PLS (PLS discriminant analysis, see Section 5.2.2) for the recognition of a chemical substructure from low-resolution mass spectral data. This type of classification problems stood at the beginning of the use of multivariate data analysis methods in chemistry (see Section 1.3). 

The effects of competition among the IR rules were explored by using the complete system, with the STIRS module disabled, to interpret the spectra of 1807 compounds from the library. For the test, we selected 500 of the 900 chemical substructures which both are chemically interesting and display at least one distinctive infrared band. Some of the selected substructures were subsets of others for example, alcohol, phenol, and primary alcohol were all in the test set. As expected, some functional groups displaying very distinctive infrared bands were detected much more reliably than others. Figure 6 shows the reliability, false positive and recall rates for a few selected functional groups. 

Figure 3. A subset of the chemical substructures database, showing the hierarchical ordering.

The program has been implemented on top of the Gorina [15] toolkit library. All chemical substructures have been hard-coded for performance reasons. The program can handle 2-D or 3-D SDFiles and will, in the latter case, produce correct 3-D coordinates for all hydrogens being changed in the process. 

Merlot, C., Domine, D., Cleva, C., and Church, D. Chemical substructures in drug discovery. Drug Disc. Today 2003, 8, 594-602. 

Information of our chemical and siRNA libraries is stored in a PostgreSQL database. We annotate our validated hits using a DatabaseReader and a Joiner node to obtain either chemical structures for chemical screens or GenelD for RNAi screens. KNIME has many tools for cheminformatics, can visualize the molecule structures, and has tools to retrieve data from external public databases via Web queries to further annotate hits, allowing clustering either by chemical substructures or GO terms. 

For example, compound selection or design on the basis of similarity to other compounds with a desired global effect on cellular gene expression is now possible -a true clinical application of systems biology. In another intriguing study, Rosania showed that chemical substructures can be predictive of subcellular distribution, which could be highly relevant to the current topic of target prediction [82]. 

Granito, Charles E., "CHEMTRAN and the Interconversion of Chemical Substructure Search Systems," Journal of Chemical Documentation, 1 3(2), 72-74 (1973). 

A number of files under the generic tide CAS ONLINE are available on-line on STN International. The system software, MESSENGER, includes chemical substructure, text, and numeric data searching facilities. Chemical structures and Registry Numbers are contained in the CA Registry file. The four ways to search the structures are EXA, FAM, SSS, and CSS. 

The National Institute of Standards and Technology s (NIST) Chemical WebBook (webbook.nist.gov/chemistry/) offers free access to ion energy and thermodynamic data for several thousand substances, and is also searchable by chemical substructure. No toxicity or environmental property data are given. 

Structure-activity relationships (SARs) and quantitative structure-activity relationships (QSARs), referred to collectively as QSARs, can be used for the prediction of physicochemical properties, environmental fate parameters (e.g., accumulation and biodegradation), human health effects, and ecotoxicological effects. A SAR is a (qualitative) association between a chemical substructure and the potential of a chemical containing the substructure to exhibit a certain physical or biological effect. A QS AR is a mathematical model that relates a quantitative measure of chemical structure (e.g., a physicochemical property) to a physical property or to a biological effect (e.g., a toxicological endpoint). 

Three main spectra collections now exist. The first is the NIST/EPA/NIH mass spectral database, which contains 190 000 spectra of 163 000 compounds [1]. This original collection of spectra and related information is produced by the National Institute of Standards and Technology (NIST) with the assistance of expert advisors from the Environmental Protection Agency (EPA) and National Institutes of Health (NIH). This library is available on CD-ROM for personal computers with integrated tools for GC/MS deconvolution, mass spectra interpretation and chemical substructure identification. This US government publication is very cheap and of very high quality. This library is widely spread in many commercial mass spectrometers. Mass spectra for over 15 000 compounds are accessible on-line [2],... 

The most frequently used techniques for a flash analysis are infrared spectroscopy and SEC. Infrared spectroscopy provides information on the chemical substructures present in the sample, while SEC gives a first indication of the molar mass range. Information on both molar mass and composition is obtained... 

Brit. 6, 420 (1970) Citations in Chemistry (SIC) Cawkell, A. E., Chem. Brit. 6, 414 (1970). Other relevant articles in this issue include Hyams, M., Chemical patents information, p. 416 and Polton, D. J., lUPAC notation in chemical substructure searching, p. 430. 

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