Chemical structure retrieval systems

Willett P (1987) A review of chemical structure retrieval systems. J Chemometrics 1 139—155. 

Willett, P. A Review of Chemical Structure Retrieval Systems . J. Chemometrics. In the press. 

The same canonical name matching used for chemical structure retrieval systems works very well also in reaction indexing systems and provides rapid retrieval. 

The structure correlation approach thus provides a link between the statics of crystals and the dynamics of reacting chemical systems. The first steps could be made without the help of computer-assisted structure retrieval systems but today the only practicable way to find details of particular structures or classes of structures is through the various databases, of which... 

The reaction database compiled on Biochemical Pathways can be accessed on the web and can be investigated with the retrieval system C ROL (Compound Access and Retrieval On Line) [211 that provides a variety of powerful search techniques. The Biochemical Pathways database is split into a database of chemical structures and a database of chemical reactions that can be searched independently but which have been provided with efficient crosslinks between these two databases. 

And last not least, we will have to see further improvements in the graphical user interfaces of software systems and the retrieval systems of databases in order to make software and databases more acceptable to the chemical community at large. Software and databases should speak the language a chemist is used to, with hand-drawn chemical structures and reaction equations, or even imderstand the spoken word - and only provide the desired information selectively, not buried in a phe of unnecessary output. 

Chemoinformatics (or cheminformatics) deals with the storage, retrieval, and analysis of chemical and biological data. Specifically, it involves the development and application of software systems for the management of combinatorial chemical projects, rational design of chemical libraries, and analysis of the obtained chemical and biological data. The major research topics of chemoinformatics involve QSAR and diversity analysis. The researchers should address several important issues. First, chemical structures should be characterized by calculable molecular descriptors that provide quantitative representation of chemical structures. Second, special measures should be developed on the basis of these descriptors in order to quantify structural similarities between pairs of molecules. Finally, adequate computational methods should be established for the efficient sampling of the huge combinatorial structural space of chemical libraries. 

The CALL facility allows the expert system to access software external to the LISP program. Included with the CALL is the name of a LISP function which handles the outside software. In the case of the fact CHEMICAL NAME, the LISP function executes a FORTRAN program which allows the user to either retrieve the structure of a previously entered compound or enter a new one. The program also breaks the chemical structure into its functional groups. When the FORTRAN program terminates, the LISP function updates the list of facts, and inserts the name into CHEMICAL NAME and the functional groups into FUNCT GROUPS. These FACTS are then available to the expert system. In this way, access to outside software is completely data driven. 

MAECIS contains five major sections that are integrated into a single system. At its center is a database management system that handles the storage and updating of data and chemical structures. Associated with this section is an information retrieval section that allows one to search the database for specific information composed of any combination of data and/or substructures. Once information is retrieved, it can be displayed on a computer terminal or sent to a printer for hardcopy output using the display section of MAECIS which includes the ability to display chemical structures in various formats. The final two sections of MAECIS allow for the manipulation of chemical structures and the calculation of various molecular properties that are related to chemical structures. 

A Chemically Oriented Information Storage and Retrieval System II. Computer Generation of the Wiswesser Notation of Complex Polycyclic Structures," Journal of Chemical Documentation, (3), 133-138 (1968). 

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. 

MDL SCREEN MDL Information Systems (San Leandro, CA, U.S.A.) Oracle -based accessible multi-platform > S100K Compound registration, assay assignment, data analysis, data storage and retrieval, easy interface with chemical structure and Oracle-based infrastructure, available on multiple desktop platforms More expensive and very hard to customize... 

---