Searching for Chemical Structures

Feldman A, Hodes, L. An efficient design for chemical structure searching. I. The screens. J Chem Inf Comput Sci 1975 15 147-52. 

The information retrieval in MAECIS is accomplished using one of three available commands SHOW, FIND, or SEARCH. The SHOW command is the simplest one to use and requires only a code number or registry number. It allows the user to retrieve all chemical structures and associated information stored under a particular code number. In most cases this fulfills the user s needs. The FIND command is used for complex searches involving various combinations of multiple data fields, handles substructure searching. Queries such structures with a molecular weight between 200 and 250 containing an ester substructure" are handled by the FIND command. Finally, the SEARCH command is used for chemical structure searches. This search takes only seconds and allows the chemist to determine if a particular molecule is already in the database. 

Feldman, Alfred, and Louis Hodes, "An Efficient Design for Chemical Structure Searching I, the Screens," Journal of Chemical Information and Computer Sciences, 15(3), 147-151 (1975). 

L. Hodes and A. Feldman, "An Effective Design for Chemical Structure Searching. II. File Organization". J. Chem. 

The Emergence of Graphics Systems for Chemical Structure Searching... 

Thus, if the user wants to look for literature including requested chemicals or reactions, it is possible to query the database by the first option Chemical Substance or Reaction , The compound can be entered as a query in three different ways drawing the chemical structure in a molecule editor (Chemical Structure) searching by names or identification number, such as the CAS Number (Structure Identifier) and searching by molecular formula (Figure 5-12). 

As already mentioned (Section 5.3), the stored structure information in this type of database makes it possible to search for chemical structures in several ways. One method is to draw a structure (via a molecule editor) and to perform either a precise structure search (full structure search) or a search containing part of the input structure (substructure search) (see Sections 6.2-6.4). The databases also allow the searching of chemical names and molecular formulas (see Section 6.1). The search results are in most cases displayed in a graphical manner. 

MDL s Chemscape Server and Chime Pro product suite is an integrated set of tools for chemical structure illustration, communication, and database searching. Chime and Chime Pro are chemical structure visualization programs that run in the most popular Web browsers. 

Databases of Three-Dimensional Chemical Structures, Searching Techniques for... 

The use of computer-readable formats for chemical structures has become a compelling need to capture this information in databases or to simply annotate documents (Degtyarenko et al. 2007). Annotating full text documents with these machine-readable forms can make documents easier to search, and the intended structure can be visualized in context. The development of computer-readable formats started in earnest around 1990 (Borkent et al. 1988 Weininger 1988 Contreras et al. 1990 Ibison et al. 1993). 

The EPO esp cenet (ep.espacenet.com) database contains more than 60 million patents from 85 conntries worldwide (not just European Convention countries). The database is searchable by application number, assignee, inventor, or keywords from the title or abstract. Chemical structure searches are not possible. Patents can be viewed as images of the original document in PDF format one page at a time, or the whole patent can be viewed as a text document. Instantaneous translation from French or German into English is available for the latter document type if required. Equivalent pnblished patents, if any, are also listed and are available in PDF format. The text documents do not show chemical structures or diagrams, but these can be viewed in PDF format if required. 

Barnard JM. Substructure Searching Methods Old and New. J. Chem. Inf. Comput. Sci. 1993 33 532-538. An overview of the chemical structure search methods used in modem databases and in databases created before the development of computers powerful enough for topological stmcture searching. 

Brown RD, Downs GM, Willett P, Cook APF. A hyperstructure model for chemical structure handling generation and atom-by-atom searching of hyperstructures. J Chem Inf Comput Sci 1992 32 522-531. 

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