Full Structure Search

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. 

To become familiar with various methods and tools for full structure recognition and the search in structural datasets. 

Full structure search can be developed by using similar approaches to those employed in the case of 2D structure search. Thus, some topological indices can be modified in such a way that they include geometrical information. For example, the global index given by Eq. (4) can be modified to Eq. (11), where are real interatomic distances. 

Figure 10.3-20 shows that i-glutamate plays an important role in the metabolism with many reactions leading to this compound and many reactions starting from it. The first example gives a full structure search in order to show how easy it is to find all reactions that a certain compound participates in. 

To seat ch for available starting materials, similarity searches, substructure searches, and some classical retrieval methods such as full structure searches, name searches, empirical formula searches, etc., have been integrated into the system. All searches can be applied to a number of catalogs of available fine chemicals (c.g, Fluka 154]. In addition, compound libraries such as in-housc catalogs can easily be integrated. 

Depending on the sophistication needed, substructure searching can be accomplished with a variety of the representations of a chemical substance. Some substructure searches can only be adequately answered by a complete atom-by-atom and bond-by-bond search for which a connection table, with its explicit description of full structural detail, is essential. 

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). 

In the PSSC procedure itself, initially the full structure of a protein of interest was subjected to search for structural similarity using the Dali (FSSP) and Combinatorial Extension (CE) algorithms. The searches were performed across the entire PDB and yielded lists of structurally similar proteins ordered by decreasing similarity (Figure 9.14). The entries which were deemed interesting... 

MolMall features the Rare Chemical Samples ExchangeCenter. Compounds are made available from small samples provided by individual researchers. Full structure search or substructure searches are permitted on the web site, as well as for the name of the submitter and several other very useful searching functions. Links to Molecules MolBank (http //www.molbank.org) papers if the compounds are published there. There are plans to allow the sample submitters to add additional information to the data sheet, such as the literature where the compound was published. 

Work currently in hand or needed for solution of the problem is described. The overall objective is to provide general facilities for full structure and for substructure searching. 

Our full structure search system determines the possible Chemical Abstracts Service (CAS) registry numbers and internal compound numbers for a given structural drawing. Additionally the user can select from a set of predefined keyword profiles and submit a job for CAS ONLINE. A minicomputer will set up the query, call the host system, perform the search, capture the answers and inform the user that the job was successfully completed. The user can now play back the answers at his terminal with structural formulae, bibliography and abstracts. The only activities are structure drawing, menu selection, waiting and scanning the results. 

Reaction retrieval deals with very precise full structure information but you have to be aware of different possible ways to define the reaction centres. Another problem is the various notations for certain functional groups (e.g., sulphur and phosphorus groups). The most restricting factor yet is the inability to search for reaction sequences. Because of this you have to guess how a one-pot reaction or a multistep sequence was stored in the database. As a consequence you miss the information (Figure 6). 

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). 

The team decided that the system software should be selected from a source that was well-established in the field of technical information. In addition, if one software and one command language could be used for the entire system, i.e., both text and chemical structure, it would be advantageous to the technical community. Because the thesaurus, a hierachical list of controlled terms, was the key to the text or document file, thesaurus software was also necessary. Search software for chemicals had to have the capability to search by substructure or full structure, by name, by compound number, by molecular formula, and by class descriptor. Continuity in both systems support and staff was a very important consideration. Another criterion was that the system be kept up-to-date with enhancements resulting from ongoing research in information science. 

Support software must be developed in each of these areas and integrated into the DBMS for every new abstract data t3q>e. For example, to create a chemical structure ADT, a storage format, such as a connection table format, must first be defined. Then operators for full structure, substructure, and other types ol structure searches must be defined. Access methods need to be implemented to provide fast structure searches and finally, the characteristics of the various structure searches must be made known to the query optimiser to allow efficient overall query execution. 

The first table supports full structure and component structure searching and has the form shown in Table 2. The RN column contains the registry number for the compound and the HASH VALUE column is a character string containing a... 

Four structure search operations are supported. Full structure and component search take advantage of the hash table for their implementation and substructure and similar-structure search use the screen table. For a full structure or component match the ADT shell creates a new SQL statement of the following form ... 

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