Structures Downloading

The National Cancer Institute (NCI) database is a freely available collection of more than 200,000 compounds and it is frequently used by research groups to perform virtual screening followed by experimental testing. Table 2.2 contains two links where it is possible to mine the database online and to download structure files for analysis. 

National Cancer Institute. Downloadable structure files of NCI open database compounds. 2007. http //cactus.nci.nih.gov/ncidb2/download.html (accessed April 18,2008). 

The enzyme aetivity of MAO is inhibited by amphetamine and ephedrine, and the enantiomers are ehirality selective. The selectivity was studied by comparing it to that of the eomplex form of DAO. The downloaded structure of MAO was earefully fixed after rejection by the MM2 program. The substrate was replaced with optimized (/ )- or (S)-amphetamine, and the complex conformation was further optimized using the MM2 program. The complexes with the lowest energy values were selected as the ideal conformations. 

Figure 2-137. Screenshot of the 3D structure viewer and download options for the 3D structure generated on the CORINA web interface.

When the button "submit smiles is pressed, the SMILES string is sent to the web server of Molsoft, converted to 3D, and the 3D structure is displayed in a java molecule viewer on an automatically created web page (see Figure 2-139). Unfortunately, the Molsoft server does not support downloading of the 3D structures in a standard file format. 

The right-hand side of the form gives the network map in the upper part and to its right the simulated IR spectrum is plotted, which can be downloaded as a JCAMP File (cf. Section 2,4.5, Section 4,2,4.2). By clicking on tbe neurons in the map one obtains the RDF code and the spectrum of the corresponding structure in the lower part of the form and compared with those of the winning neuron,... 

The structure of human muscle fructose-1,6-bisphosphate aldolase, as determined by X-ray crystallography and downloaded from the Protein Data Bank. (PDB ID 1ALD Gamblin, S. J., Davies, G. J., Grimes, J. M., Jackson, R. M., Littlechild, J. A., Watson, H. C. Activity and specificity of human aldolases. J. Mol. Biol. v219, pp. 573-576, 1991.)... 

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 US EPA T.E.S.T. is a downloadable program to estimate different toxicological endpoints and physicochemical properties from molecular structure using a variety of QSAR methodologies [58],... 

J. Sanyova, Contribution a l etude de la structure et des proprietes de la laque de garance, PhD Thesis, Bmssels, 2001. Downloadable from http //theses.ulb.ac.be/ETD db/collection/available/ULBetd 08092006 162429/. 

Fig. 31. Molecular structure of 40h in the crystal. This figure was generated using data downloaded from The Cambridge Crystallographic Data Centre (CCDC) and corresponds to a structure originally reported in Ref. (212).

MDL Information Services, Inc. offers free software downloads at http // www.mdli.com/cgi/dynamic/downloadsect.html7uid= key= id = 1. These include AutoNom Standard (automatic nomenclature), which generates IUPAC chemical names directly from graphical structures created in ISIS/Draw or registered in ISIS/ Base. 

Crystal structures are best viewed as three-dimensional computer images that can be rotated and viewed from any direction. Crystal structures can be displayed, and downloadable programs for graphical presentation of crystal structures can be found at the EPSRC s Chemical Database Service at Daresbury. This can be accessed at http //cds.dl.ac.uk/ cds. See also ... 

Domain Where Physics, Chemistry, Biology, and Technology Meet (see above) p. 11. The paper, Use of quantitative structure-property relationships in predicting the Krafft point of anionic surfactants by M. Jalali-Heravi and E. Konouz, Internet Electronic Journal of Molecular Design, 2002, 1, 410, has a nice introduction and useful references. It can be downloaded at http //www.biochempress.com/av01 0410.html. 

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