Reaction databases types

A wider variety of reaction types involving reactions at bonds to oxygen atom bearing functional groups was investigated by the same kind of methodology [30]. Reaction classification is an essential step in knowledge extraction from reaction databases. This topic is discussed in Section 10.3.1 of this book. 

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. 

Reactions can be considered as composite systems containing reactant and product molecules, as well as reaction sites. The similarity of chemical structures is defined by generalized reaction types and by gross structural features. The similarity of reactions can be defined by physicochemical parameters of the atoms and bonds at the reaction site. These definitions provide criteria for searching reaction databases [23],... 

Chemical information is reported and recorded in many forms, and a wide vnriety of databases have evolved to collect the various types of informalion. Bibliographic, business, structure, numeric, spectra, and reaction databases currently arc available. 

The second large reaction database is Chemical Abstracts from the American Chemical Society, accessed most often via the Scifinder interface. It basically suffers from the same limitations as mentioned above. The main advantage of Scifinder for combinatorial chemists is the ability to also search for keywords. Thus, a search for a specific reaction type combined with keywords such as solid phase or immobilized reagent often leads to useful literature citations. 

Enzyme-Reaction Database. We have built a database called the Enzyme-Reaction database for drug design based on amino acid sequence (Nishioka and Oda, unpublished). This database contains the following Items for each enzyme enzyme name Including common names, EC-number and reaction type classified by TUB, names of substrates, cofactors, inhibitors, and products, and entry codes in the NBRF sequence database and the Brookhaven Protein Databank. 

The database contains 3500 reactions, 85 types of mechanism as well as the chemical parameters related to them. Approximately 500 - 700 reactions are added each year. 

An analysis of the ORAC CORE reaction database of over 50,000 reactions shows that approximately 15% of the reactions are linked to other reactions via implicit links. We estimate that there are about 25,000 implicit links between reactions in the ORAC CORE database. However, implicit links between reactions in different selective databases are much less common due to the variation in the type of chemistry and examples used. The distribution of links between reactions is very dependent on the reactant and product structures. Common reactants, such as benzaldehyde, may account for a relatively high percentage of implicit links in a reaction database. 

Two other types of molecular database are pertinent to drug discovery. One is the so-called reaction database. It is a 2D database containing the reagents, products, and conditions of chemical reactions. The medicinal chemist would use one of these databases as a resource to find synthetic procedures. Another type of molecular database used in pharmaceutical and biotechnology research contains peptide sequences of proteins and nucleic acid base sequences of DNA and RNA. These sequence databases are essential in biotechnology and genomics, which have their role in modem dmg discovery. 

The integrated databases are divided in this approach into structural and reaction databases. Other types of integrated databases are spectral databases and patent databases. Patent databases have an increasing importance in environmental questions related to technology. ... 

These chemical reaction databases contain not only reaction-type data, but also in most cases, bibliographic or factual information as well. 

This description sees the elements of the database as structures linked to properties linked to references, and a chemical reactions database is included . This reflects exactly the historical development of the Beilstein Handbook, and later the Beilstein file on STN and DIALOG these collections are lists of compounds, with subsections on property type, linked to sub-subsections of reference lists. But the CrossFire implementation is much more than this. It has a different data orientation, and can justly be regarded as a new implementation, in fact a... 

All three types can be described by (sub)structures and roles plus mapping/reaction centers. Type 2 and, in particular, type 3 are also suitable for keyword searching if the database contains keywords for compound classes/liuictional groups/reaction types (see Section 4.11). 

The in-house systems REACCS, ISIS, and CrossFire handle aromaticity and tautomerism satisfactorily a user can enter structures as any chemist normally would without having to worry about the bond conventions used internally by the database system. This is not yet true for CASREACT and other reaction databases offered under STN Messenger. Here the user has to know the definition and use of normalized bonds, a special bond type defined to handle aromaticity and tautomerism in a formal way. This, unfortunately, corresponds only partially to these concepts ias used by chemists. CAS is working on Ais problem the SciFinder interface already offers a solution for exact structures, but not yet for substructures, falling into this category (see Structure Representation). 

In order to create subsets of this large reaction file, which can be searched on-line via STN International or with commercial in-house retrieval systems such as REACCS/ISIS from MDL Information Systems, Inc. (USA), a sophisticated algorithm has been developed by InfoChem which identifies the different reaction types in this large database. This InfoChem Classification Algorithm is currently the only available concept for structuring large reaction databases and has, therefore, a high commercial value. 

Since many of these 2.5 million reactions of the InfoChem Reaction Database are variations of the same type of reaction, InfoChem has developed a sophisticated selection concept based on the identification of all the different individual reaction types included in this file. This so-called Classification Algorithm is also used by MDL Information Systems, San Leandro, CA. Reactions with identical reaction centers and neighboring atoms are considered to be of one reaction type. An analysis of the 2.5 million reactions led to the identification of over 390 000 different reaction types. In the ChemReact database each reaction type is represented by only one selected example reaction. ChemReact was further refined to create ChemSynth, ChemReactlOO, and ChemReact41. 

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