Corporate chemical structure databases

As mentioned above, corporate chemical structure databases are replete with analog series and are thus far from representative of the full range of structural or physicochemical diversity. There is therefore much interest in, first, locating the diversity voids within a particular collection, and then analyzing external collections to see which compounds could be purchased to occupy those holes. In this way, the molecular diversity of a corporate collection can be enhanced, and this in turn should lead to better results from high-... 

Today, pharmaceutical companies are linking CDS to business systems such as SAP, chemical structure databases, electronic laboratory notebooks, and corporate data warehousing solutions. Many commonly used software products utilize COM Automation (Microsoft s Component Object Model) to provide a powerful array of programmable objects that allow seamless connections between applications. 

This section will describe examples of a variety of different types of 2D and 3D chemical structure databases and data collections. These range from comprehensive collections of small organic molecules (CAS registry file and Beilstein), to specialized collections of analytically derived 3D structures (CSD and PDB), to commercial reagent catalogs (ACD), to prospective and actual pharmaceutical entities (MDDR, NCI, and the typical corporate pharmaceutical database). Access to all but proprietary collections is available for a fee. For additional information, see also Online Databases in Chemistry. 

Database of Chemical Structures and Property Predictions. ChemZoo Corporation (http //www.chem spider.com/). 

Pre-1980 —Flat File Storage of Chemical Structures. Computers consisted of mainframe machines (e.g., IBM 3090) and small minicomputers (Digital, Prime). Users connected through low speed serial connections, using "dumb" terminals (no graphics capability) or monochrome vector graphics terminals such as Tektronix and Imlac. Chemical structures were mainly stored as either (l)individ-ual structure files, indexed by name, and handled one or a few structures at a time or (2) in a flat-file database accessed by record number (26). A typical corporate database contained up to a few tens of thousands of structures. 

To optimise the use of chemical structures stored in computer databases, Ciba-Greigy s Pharmaceuticals Division follows the following general strategies it maintains a corporate file of all compounds synthesised by all divisions and it maintains division-specific databases containing all compounds ever synthesised and tested. These are accessible by all research centres world-wide. Associated with the chemical structures which are stored in MACCS, is a minimal set of non-relational information. Additional batch-specific data such as physico-chemical properties are stored in a linked ORACLE... 

Figure 12. A pictorial view, and the HView definition, of two distributed molecule databases, named CORPORATE, and FCD, respectively. In the absence of a linking field such as a registry number common to both databases, the linking field is specified as chemiced structure. Identity of chemical structures is used to satisfy the equality required by the hnk...

AIA = Analytical Instruments Association AFFN = ASCII free format numeric API = application programming interface ASDF = ASCII squeezed difference form ASMS = American Society of Mass Spectrometry ASTM = American Society for Testing and Materials CCDB = Committee on Chemical Databases CDF = common data form CPEP = Committee on Printed and Electronic Publications CS = chemical structure EPA = United States Environmental Protection Agency lUPAC = International Union of Pure and Applied Chemistry JCAMP-DX = Joint Committee on Atomic and Molecular Physical Data - Data Exchange LDR = labeled data record netCDF = network common data form SMD = standardized molecular data UCAR = University Corporation for Atmospheric Research XDR = external data representation. 

The greatest benefit of RACHEL S component extraction method is that a massive property index of the entire corporate database is created. Along with the atomic coordinates of each component, a wealth of chemical information characterizing each building block is stored. Data such as the size of the component, atom composition, connectivity, ring structure, and electrostatic charges are included. As such, a means of rapidly cross-referencing chemical components on demand is available. 

As we have shown in this example, the use of templates and chemical descriptors allows RACHEL to generate chemically diverse ligand derivatives within specific user constraints. In addition, building structures from enriched corporate database fragments... 

Today, most data are entered into corporate databases which consider the need of the user and the purpose of data. They are structured, searchable, contain both raw and metadata. Decision-making tools can mine these databases and if necessary combine data from various sources, including genetic, proteomic, clinical and chemical databases. 

Most corporate databases of chemical compounds (libraries) are of the 2D type. The databases are managed using software that allows fast registration of new structures, fast retrieval of previously stored compounds, and fast substructure searching. (For more information about chemical database management software, see www.mdl.com or www.daylight.com.)... 

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