Reaction retrieval compound databases

Figure 2 Reaction retrieval from reaction and compound databases...

In this section, the basic concepts of reaction retrieval are explained. The first example is concerned with finding an efficient way to reduce a 3-methy]cydohex-2-cnonc derivative to the corresponding 3-mcthylcyclohcx-2-cnol compound (see Figure 5-24). As this is a conventional organic reaction, the CIRX database should contain valuable information on how to syntbesi2e this product easily. 

Reaction retrieval systems are usually built without due connection with systems built earlier for the retrieval of compounds. This paper discusses options for a file organisation for a unified structural database of compounds and their reactions. Such a database has a potential for improved retrieval capabilities and high browsability. 

This simple classification of reaction queries illustrates the need for both comprehensive and selective reaction (and sometimes even compound) databases. There is some disagreement among chemical information specialists about whether there will still be a need for selective reaction databases in the future, in view of the expected enhancement of retrieval and post-processing procedures in large reaction databases (see Sections 4.2, 4.11, and 5). 

Compounds are stored in reaction databases as connection tables (CT) in the same manner as in structure databases (see Section 5.11). Additionally, each compound is assigned information on the reaction center and the role of each compound in the specific reaction scheme (educt, product, etc.) (see Chapter 3). In addition to reaction data, the reaction database also includes bibliographic and factual information (solvent, yield, etc.). All these different data types render the integrated databases quite complex. The retrieval software must be able to recall all these different types of information. 

The reaction database compiled on Biochemical Pathways can be accessed on the web and can be investigated with the retrieval system C ROL (Compound Access and Retrieval On Line) [211 that provides a variety of powerful search techniques. The Biochemical Pathways database is split into a database of chemical structures and a database of chemical reactions that can be searched independently but which have been provided with efficient crosslinks between these two databases. 

The reaction databases let scientists easily and quickly retrieve information about the chemistry of known substances, some of which might be similar to the investigational compounds under study in forced degradation testing. Many of the readers of this book will already be acquainted with these informatics resources on their desktop computers. 

A module of the CHEM-X modelling system (see modelling section). Storage and retrieval of two- and three-dimensional structures with substructure-search capability. Available databases include Chapman Hall Dictionary of Drugs (15,000 compounds). Chapman Hall Dictionary of Fine Chemicals (120,000 small organics). Chapman Hall Dictionary of Natural Products (54,000), Derwent Standard Drug File (31,000 biologically active compounds), ChemReact (370,000 reaction types) and others. 

While an OOP representation is flexible, it nonetheless encompasses an overall view, i.e., the designer s vision of the general nature (but not the details) of the computational methods that will rely on the representation. Here, the scope envisioned for the representation of biochemical pathways is defined to include the following general goals. The system should function as a biochemical database, allowing the storage and retrieval of commonly available types of data for biochemical compounds, reactions, pathways, and enzymes. For each type of object, a different set of data must be available and easily accessible,... 

In 1982, MDL started selling REACCS, a database management system for chemical reactions. Medicinal chemists liked both MACCS and REACCS. The former could be used to check whether a compound had been synthesized in-house and, if so, how much material was left in inventory. The latter program could be used to retrieve information about synthetic transformations and reaction conditions that had been published in the literature. 

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