Structure and Substructure Searching

Factual databases may provide the electronic version of printed catalogs on chemical compoimds. The catalogs of different suppliers of chemicals serve to identify chemical compounds with their appropriate synonyms, molecular formulas, molecular weight, structure diagrams, and - of course - the price. Sometimes the data are linked to other databases that contain additional information. Structure and substructure search possibihties have now been included in most of the databases of chemical suppliers. 

Besides structure and substructure searches, Gmclin provides a special search strategy for coordiuation compouuds which is found in no other database the ligand search system, This superior search method gives access to coordination compounds from a completely different point of view it is possible to retrieve all coordination compounds with the same ligand environment, independently of the central atom or the empirical formula of the compound. 

Mathematical theory of labeled colored graphs is exclusively used to formalize the structure and substructure search problem. There is almost a one-to-one correspondence between the terms used in graph theory and the ones used in chemical structure theory. Formally a graph G can be given by Eq. (1), where V is the set of graph vertices and H the set of edges. 

Structure and substructure searching are very powerful ways of accessing a database, but they do assume that the searcher knows precisely the information that is needed, that is, a specific molecule or a specific class of molecules, respectively. The third approach to database searching, similarity searching, is less precise in nature because it searches the database for molecules that are similar to the user s query, without formally defining exactly how the molecules should be related (Fig. 8.3). 

Circular substructures of various sorts have been widely used for applications such as structure and substructure searching, constitutional symmetry, structure elucidation and the probabilistic modeling of bioactivity inter alia The work reported here demonstrates that this type of fragment is also very well suited to virtual screening using multiple reference structures. 

Structure searching and display software are host-specific. The Softon Substructure Search System (S4) was developed by the Beilstein Institute and Softon of Graefelfing Germany (50). It is a full structure and substructure searching module. The S4 is used in-house by the Beilstein Institute and is operated by DIALOG. STN uses CAS ONLINE s messenger software for on-line structure searching of the Beilstein on-line database (51). 

CAS/STN International. CAS/STN offers structure searchable files such as Registry, Beilstein, MARPAT, CASREACT, and Gmelin a variety of learning files, eg, LRegistry, LBeilstein, LMARPAT, and LCASREACT and software products such as STN Express for on-line structure and substructure searching. Chemical Abstracts Service, a division of the American Chemical Society, has published Chemical Abstracts since 1907 and joindy operates STN International with FIZ Kadsruhe and the Japan Information Center of Science and Technology. 

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). 

Cohan, P., "Current Technologies in Chemical Structure and Substructure Searching Using Microcomputers" Online 87 Information Proceedings, Learned Information, New Jersey, 8-10 December 1987, pp 533-545. 

Xu, J. (2003) Two-dimensional structure and substructure searching, in Handbook of Ghemoinformatics, Vol. 2 (ed. J. Gasteiger), Wiley-VCH Verlag GmbH Weinheim, Germany, pp. 868-884. 

The foundations of graph theory and algorithms required for structure and substructure searching are reviewed by Hopkinson. ... 

The structures of the Beilstein compounds are stored in connection tables (CT s) to allow a very flexible structure and substructure search. Since most commercially available structure/substructure handling programs such as MACCS (MDL) or DARC (Telesystemes/Questel) work on the basis of CT s, the Beilstein Registry Connection Table (BRCT) can be easily adapted for in-house systems. 

One of the earliest examples of a proprietary CIDBS was begun at The Upjohn Company in 1974. The initial goal was a basic one create a system that would allow the company s 50,000 structures to be drawn in and stored in a database in their native graphical form and searched via graphically entered full structure and substructure search queries. Search response was expected to be interactive (i.e., less than 30 sec per substructure search). 

Searches on all text and numerical indexes, as well as structure and substructure searching can be carried out on the CD-ROM version of the Dictionary. In the CD-ROM Type of Compound Index, all carbohydrates in the Dictionary are classified under one or more of the headings given in Fig. 2. 

SciFinder. SciFinder is an interface to the Chemical Abstracts family of databases. The CAPLUS file is the equivalent to the printed Chemical Abstracts from 1907 to the present. The Registry file of chemical substances is described above. CASREACT is a file of single- and multistep organic reactions drawn from selected organic journals. SciFinder provides a user-friendly, graphical interface that permits searching by topic, author, chemical structure, and substructure. Search results can be refined, analyzed, and displayed in a number of ways. SciFinder also provides links to the electronic full text of many papers. 

The systems analysis showed that it was important for Dialog to adopt a fully integrated subsystem that would effectively perform structure and substructure searches. Such a subsystem would permit the Dialog program to remain in control of all the communications functions to the user s terminal, but would use searching techniques that were different from those of Dialog and more appropriately suited to the handling of structure information. 

Inorganic Three-dimensional Structure Databases Molecular Docking and Structure-based Design Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases Structure Representation Three-dimensional Structure Searching,... 

In a chemical documentation system, each substance must be characterized by a unique name. This unique name is used for storage, retrieval, and comparison of che-mical compounds. The nomenclature systems used by humans to communicate chemical information are not fit for computer manipulation, and special chemical structure representations are developed for chemical database management and searching (see Structure and Substructure Searching and Structure Databases). 

Representation and Manipulation Structure and Substructure Searching Structure Databases Structure Determination by Computer-based Spectrum Interpretation Structure Generators Structure Representation Symmetry in Chemistry Synthesis Design Topological Indices. 

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