Retrieval using Substructure Searching

Auto Search This button initiates from a structure query two or three automated series of search exact and substructure searches in local desktop versions exact, substructure and similarity searches in network version (under ISIS/Host). All the result lists are saved in CHIRBASE using exact-auto , SSS-auto and SIMXX %-auto names. XX is the highest similarity search value (from 80 % to 40 %) allowing to retrieve hits in CHIRBASE. The records in all the lists are unique. The SSS-auto list does not include records that are in the exact-auto list. The SIMXX %-auto list does not include records that are in exact and SSS-auto lists. 

Although an exact search can be useful, in most cases it does not give any more information than can be obtained from the printed CA. Substructure searches (SSS) are far more important, because there is no other way to get this information. If we do a substructure search on 4 in Figure A.l, we not only get all the answers we would get in an exact search, but all substances that contain, anywhere within their structure, the arrangement of atoms and bonds shown in 4. For example, 5,6,7, and 8 would all be retrieved in this search, but 9 would not be. The SSS searches typically retrieve from tens to hundreds of times as many answers as exact searches of the same stracture. Furthermore, the scope can be widened by the use of variable nodes. For example, the symbol X means any halogen, the symbol M any metal, and the symbol G allows the user to specify his or her own variable at that point (e.g., G =C1 or NO2 or Ph). As with an exact search, each answer can be displayed as described above. 

Current chemical information systems offer three principal types of search facility. Structure search involves the search of a file of compounds for the presence or absence of a specified query compound, for example, to retrieve physicochemical data associated with a particular substance. Substructure search involves the search of a file of compounds for all molecules containing some specified query substructure of interest. Finally, similarity search involves the search of a file of compounds for those molecules that are most similar to an input query molecule, using some quantitative definition of structural similarity. 

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. 

EXA (exact) search retrieves the input structure and its stereoisomers, homopolymers, ions, radicals, and isotopically labeled compounds. FAM (family) search retrieves the same structures as EXA, plus multicomponent compounds, copolymers, addition compounds, mixtures, and salts. SSS (substructure) search uses a range of possible substituents and bonds in the input structure. CSS (closed substructure) search is a more restrictive... 

Structure and Nomenclature Search System. This system links the collection of chemical databases found in the Chemical Information System (CIS), one of the first interactive systems for structure and substructure searching. References from the separate files can be retrieved by SANSS using CAS Registry Numbers, and the database of structures may be searched for structures or substructures. An adaptation of the SANSS software for substructure searching has been incorporated in the Dmg Information System of the National Cancer Institute for its own use (54). 

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.)... 

Two methods are commonly applied for library searches. Identity or retrieval searches assume that the spectrum of the unknown compound is present in the reference library, and only experimental variability prevents a perfect match of the unknown and reference spectra. When no similar spectra are retrieved the only information provided is that the unknown spectrum is not in the library. Similarity or interpretive searches assume that the reference library does not contain a spectrum of the unknown compound, and are designed to produce structural information from which identity might be inferred. Interpretive methods typically employ a predetermined set of spectral features, designed to correlate with the presence of chemical substructures. Searching identifies the library spectra that have features most similar to those of the unknown spectrum. The frequency of occurrence of a substructure in the hit list is used to estimate the probability that it is present in the unknown compound. Two well-developed interpretative search algorithms are SISCOM (Search of Identical and Similar Compounds) and STIRS (the Self-Training Interpretive and Retrieval System) [174-177]. Normally a retrieval search is performed first, and when the results are inconclusive, an interpretive search is implemented. In both cases, success depends on the availability of comprehensive libraries of high-quality reference spectra [178]. 

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