Structures Systems Searching

A hopefully complete bibliography of gas electron diffraction literature (from the very beginning through 1979) is expected to appear in the near future as a result of the activity of the Ulm center. A computerized storage and retreavel system of annotated bibliography is under way. This system will be capable to answer a great variety of questions that may occur in molecular structure literature search. 

PubChem is organized as three linked databases within the NC8I s Entrez information retrieval system. These are PubChem Substance. PubChem Compound, and PubChem BioAssay. Pubchem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links above. 

The new versions of DfW are compatible with Microsoft Windows. For the prediction of toxicity the chemical structure of a compound is input into the system with the use of ISIS/Draw (from MDL Information Systems) or by importing a mol-file or sd-file (Figure 2a). After the system has the structure, pushing the process button starts the prediction. During processing, the system searches and identifies all known toxicophores in the structure from all the different toxicological endpoints within seconds. After completion of the analysis, the system opens a result window. The result window contains the imported structure, a list of toxicological endpoints that the system has made a prediction for, the number and name of... 

A subsidiary goal from the outset was to identify those systems in which the lone-pair electrons present in these subvalent species show no stereochemical activity that is, in which the fourth-group atoms occupy sites of perfect symmetry in the solid state. Our search brought forth various scattered examples of such structural systems, and reading of their unusual properties heightened our interest. However, with the fortuitous synthesis by C. Janiak in our own laboratory... 

The mentioned data management systems are only first steps toward comprehensive lipid databases and global lipid networks. An example for such a data bank is LIPIDMAPS (http //www.lipidmaps.org), which covers structures and annotations of biologically relevant lipids (43). The structures originate from the core laboratories of the LIPIDMAPS consortium and their partners. In this database, users can search the LIPID MAPS proteome database using either text-based or structure-based search options. In addition to LIPIDMAPS, other databases in Europe (http //www.lipidomics.net) and Japan (http //www.lipidbank.jp) have been initiated. 

J.E. Ash,IT. A. Warr, andP. Willett, Chemical Structure Systems Computational Techniques for Representation, Searching, and Process of Structural Information, Ellis Norwood, New York, 1991. 

Notation Systems. Specific aspects of significance may be recorded independently within a unique code representation, as is done by several codes for molecular structure. Thus searching operations may be directed to the total compound, to various substituent groups, or to individual symbols or combinations... 

One of the first approaches for substructure search was published by Feldmann et al. [7]. They used connection table representations of 2D chemical structures to search for particular substructures within these larger structures. The resulting system — the National Institutes of Health-Environmental Protection Agency (NIH-EPA) Chemical Information System — started in 1973 as a joint project in mass spectrometry and structure searching between the NIH and the EPA [8]. 

Another major characteristic of front end systems briefly mentioned in the context of query uploading is the ability to perform query translation. In general, each host computer uses its own own command language and, particularly in the field of bibliographic and other textual data bases, a query translator is desirable to ensure that a particular query can be searched against the many and varied relevant files on diverse host computers. In chemical structure systems, the only query translator available to date is TopFrag... 

The structure editor had two modes which differed only slightly the normal mode (used to define structures to be entered into the database system) and a query mode (for entering structures for searching the database) In query mode, some options were disabled (such as attachment points and ill-defined fragments) Multivalued atom nodes and a large list of bond types were allowed in query mode In the same manner, in non-query mode, atoms must be singular valued and bond types could only be single, double, triple, stereo-up, stereo-down, or stereo-unknown ... 

MOLMOUSE will be used as an input device for the Beil stein Structure/Substructure Search System currently under development. Both the PC- and the mainframe-based version of this system will use MOLMOUSE for input. 

Computer-based chemical information systems are now widely used for the storage and retrieval of chemical structure information. Efficient searching algorithms are available which allow structure-based searches to be carried out on databases containing many thousands, or even millions, of chemical compounds. In addition, the ease with which machine-readable structural data can be manipulated has led to a wide range of related activities, such as computer-aided s)uithesis design and studies of quantitative structure-activity relationships (QSAR). ... 

Fewer than 15 years ago, after the demonstration of independent vomeronasal and olfactory system projection pathways (Winans and Scalia, 1970), the mammalian vomeronasal organ was a structure in search of a function. Clearly, our knowledge of the vomeronasal system has increased dramatically. This chemosensory system now appears to be critical for learning... 

Ash JE, WarrWA, Willett P (1991) Chemical structure systems computational techniques for representation, searching, and process of structural information. Ellis Horwood, New York Gluck DJ (1964) A chemical structure storage and search systems developed at Du Pont. J Chem Informat Model 5 43-51... 

The idea of de novo structure elucidation is to find the correct structure without searching databases. A prominent starting point is the well known DENDRAL system [183], the development of which began already in the mid 1960 s. DENDRAL was developed for the automated structure elucidation of organic compounds by MS, after separation by gas chromatography (GC). 

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