Substructure searching definition

Table 3.1. Alphanumeric instruction set for 2D substructure search definition within CSD System Versions 3 and 4...

Figure 10.3-54 illustrates how the reaction center is derived from the disconnection of the strategic bond and which additional bond spheres are considered in the definition of the reaction substructure search queiy. 

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. 

A handful of tables that contain database parameters. These include substructure search key definitions, the periodic table used with the database, and a list of salt moieties that can be considered during searches. 

ConQuest provides search, retrieval, and display facilities for the CSDJ Individual queries can be set up to interrogate the bibliographic, chemical text, and crystal data fields listed in Table 2, and, in particular, the program provides extensive graphical facilities for the definition of 2D and 3D substructure searches. The 2D searches interrogate the chemical connection tables alone, while... 

A recent study has compared the NCI-DCT system with the NIH-EPA Chemical Information System for the ability to perform substructure searches of large files of compounds (22). The Merck modification of the Walter Reed Army Institute of Research substructure search system was also compared. This report should be referred to for a detailed analysis of these major substructure systems. Another system, prepared with a smaller computer and a smaller set of chemicals, has been developed by Jurs and colleagues 23). All of these systems can be readily used in substructural analysis studies. It would appear that the exact coding system used in such studies is not critical, but no definitive comparisons of these systems for SAR utility have been performed. 

By definition, any query which is a substructure of the candidate, will give a similarity value of 100. In this sense, a sub-similarity search can be viewed as a fiizzy substructure search. 

In the case of the second problem, however, it is both possible and desirable to give a definition of the search tool, and that is the purpose of this paper. The LN is a flexible and useful tool, but contains the seeds of much difficulty if the concept is applied incautiously. It is not a type of substructure searching, nor is it a Markush search. To repeat the above objective once more, the intention behind the LN is to retrieve those sorts of structures which one might have found within a few pages of the given structure, had the user been looking in an Omnibus Edition of the Beilstein Handbook. 

The functionality required for an ELN to handle these structures is a specialized structure editor allowing creation and visualization of residues, definition of residues as real structures, and combined search for substructures in both the compound and the residue. Some additional features in the structure viewer help to mark and emphasize residues of the structure, allow overlapping residues, and label residues. A flag indicates whether the residues are displayed in the current context or not. If more than one residue is available, it is possible then to show or hide individual residues of a structure. The structure editor may be independent of a primary editor that is able to handle complete structures that is, structures are created with an external standard editor, whereas residue definitions are performed with an embedded tool. Since most databases are not designed for storing incomplete information, an ELN has to provide an internal format to store incomplete structures. In fact, it stores every complete part of a structure in a conventional database and keeps the additional information about the missing parts. 

---