Of chemical structures

To learn more about connection tables and matrix representations of chemical structures... 

In chemistry, chemical structures have to be represented in machine-readable form by scientific, artificial languages (see Figure 2-2). Four basic approaches are introduced in the following sections trivial nomenclature systematic nomenclature chemical notation and mathematical notation of chemical structures. 

A connection table has been the predominant form of chemical structure representation in computer systems since the early 1980s and it is an alternative way of representing a molecular graph. Graph theory methods can equally well be applied to connection table representations of a molecule. 

Figure 2-23. Transformation of representations of chemical structures between chemists and computers,...

In the ancient times" the 1950s), data were transferred to computers by using punched cards. But already in 1959 Ascher Opier from Dow Chemical Company reported the use of a light pen for graphical entiy of chemical structures into a computer. Light pens were also used in the Chemical Abstracts Service in the 1970s. 

In 1964 Douglas Cart Engelbart (Stanford Research Institute in California) developed the mouse as an input device and Bill Enghsh built its prototype from a carved block of wood with a single red button. Shortly thereafter, the mouse was used at the Lister Hill Center of the National Institutes of Health for the input of chemical structures. 

The different internal and external file formats make it necessary to have programs which convert one format into another. One of the first conversion programs for chemical structure information was Babel (around 1992). It supports almost 50 data formats for input and output of chemical structure information [61]. CLIFF is another file format converter based on the CACTVS technology and which supports nearly the same number of file formats [29]. In contrast to Babel, the program is more comprehensive it is able to convert chemical reaction information, and can calculate missing atom coordinates [29]. 

Table 2-5. The most important File formats for exchange of chemical structure information.

Over and beyond the representations of chemical structures presented so far, there are others for specific applications. Some of the representations discussed in this section, e.g., fragment coding or hash coding, can also be seen as structure descriptors, but this is a more philosophical question. Structure descriptors are introduced in Chapter 8. 

This ambiguous representation of chemical structures as a string allows a veiy efficient similarity search,... 

Walking through the Hierarchy of Chemical Structure Representation... 

Before we go into further detail on the handling of chemical structures in 3D space from the chemoinformatics point of view, it should be noted that there... 

In the mid 1970s, Ugi and co-workers developed a scheme based on treating reactions by means of matrices - reaction (R-) matrices [16, 17]. The representation of chemical structures by bond and electron (BE-) matrices was presented in Section 2.4. BE-matrices can be constructed not only for single molecules but also for ensembles of them, such as the starting materials of a reaction, e.g., formaldehyde (methanal) and hydrocyanic add as shown with the B E-matrix, B, in Figure 3-12. Figure 3-12 also shows the BE-matrix, E, of the reaction product, the cyanohydrin of formaldehyde. 

To become familiar with the basics of chemical structure similarity, similarity measures, and different approaches exploited within the similarity search process. 

Any development of chemical structure perception methods must obey the following requirements ... 

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],... 

A substructure search algorithm is usually the first step in the implementation of other important topological procedures for the analysis of chemical structures such as identification of equivalent atoms, determination of maximal common substructure, ring detection, calculation of topological indices, etc. 

A most important task in the handling of molecular data is the evaluation of "hidden information in large chemical data sets. One of the differences between data mining techniques and conventional database queries is the generation of new data that are used subsequently to characterize molecular features in a more general way. Generally, it is not possible to hold all the potentially important information in a data set of chemical structures. Thus, the extraction of relevant information and the production of reliable secondary information are important topics. 

Finding the adequate descriptor for the representation of chemical structures is one of the basic problems in chemical data analysis. Several methods have been developed in the most recent decades for the description of molecules including their chemical or physicochemical properties [1]. 

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 comparison For identity of chemical structures is peiTormed on the basis of a hashcode algorithm, Hashcode are unique integer numbers which can be calculated for each chemical structure within the WODCA system [55], Further exam-... 

With better hardware and software, more exact methods can be used for the representation of chemical structures and reactions. More and more quantum mechanical calculations can be utilized for chemoinformatics tasks. The representation of chemical structures will have to correspond more and more to our insight into theoretical chemistry, chemical bonding, and energetics. On the other hand, chemoinformatics methods should be used in theoretical chemistry. Why do we not yet have databases storing the results of quantum mechanical calculations. We are certain that the analysis of the results of quantum mechanical calculations by chemoinformatics methods could vastly increase our chemical insight and knowledge. 

Downs G M, P Willett and W Fisanick 1994. Similarity Searching and Qustering of Chemical Structure Databases using Molecular Property Data, journal of Chemical Information and Computer Sciences 34 1094-1102. 

Downs G M and Peter Willett 1995. Similarity Searching in Databases of Chemical Structures. In Lipkowitz K B and D B Boyd (Editors) Reviews in Computational Chemistry Volume 7. New York, VCH Publishers, pp. 1-66. 

Livingstone, D 2000. The Characterisation of Chemical Structures Using Molecular Properties. A Survey. Journal of Chemical Information and Computer Science 40 195-209. 

Chem3D can read a wide variety of popular chemical structure files, including Gaussian, MacroModel, MDL, MOPAC, PDB, and SYBYL. Two-dimensional structures imported from ChemDraw or ISIS/Draw are automatically converted to three-dimensional structures. The Chem3D native file format contains both the molecular structure and results of computations. Data can be exported in a variety of chemical-structure formats and graphics files. 

Another important area of analytical chemistry, which receives some attention in this text, is the development of new methods for characterizing physical and chemical properties. Determinations of chemical structure, equilibrium constants, particle size, and surface structure are examples of a characterization analysis. 

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