Chemical structure coding

Until the late 1970s, the Wiswesser Line Notation (WLN) was the only widely recognized format in which to code chemical structures in a computer-readable linear format. It was invented by William J. Wiswesser (1952), and his work was recognized and honored with the Skolnik Award for outstanding contributions to and achievements in the theory and practice of chemical information science by the American Chemical Society in 1980. The WLN was quickly adopted by major chemical companies to store and retrieve machine-readable, 3D-chemical structure information in a 2D, linear array, and is still in use today. 

Hosoya, H. (1972c). Topological Index as a Sorting Device for Coding Chemical Structures. J.Chem.Doc., 12,181-183. 

Hosoya, H. (1972c) Topological index as a sorting device for coding chemical structures. J. Chem. Doc., 12, 181-183. 

The chemical markup language (CML) is based on the extensible markup language (XML) in order to code chemical structures [21-24], Besides chemical structures and reactions, CML is capable of drawing spectra, etc. 

The IFI Comprehensive (CDB) code currently in use was created in 1972 by the merger of a DuPont coding system that commenced indexing of US patents in 1964, and an IFI code that began coding chemical structures in US patents in 1950. Most of the Markush codes in the present CDB are from the DuPont system, so the Markush backfile really only dates to 1964. Earlier coverage from the IFI system was limited to specific compounds and general terms. The IFI code is still... 

Sample code Chemical structure of surfactant d-spadng (nm)... 

The ROSDAL syntax is characterized by a simple coding of a chemical structure using alphanumeric symbols which can easily be learned by a chemist [14]. In the linear structure representation, each atom of the structure is arbitrarily assigned a unique number, except for the hydrogen atoms. Carbon atoms are shown in the notation only by digits. The other types of atoms carry, in addition, their atomic symbol. In order to describe the bonds between atoms, bond symbols are inserted between the atom numbers. Branches are marked and separated from the other parts of the code by commas [15, 16] (Figure 2-9). The ROSDAL linear notation is rmambiguous but not unique. 

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. 

Hash codes of molecules which are already pre-computed are suitable for use in fiill structure searches in database applications. The compression of the code of a chemical structure into only one number also makes it possible to compute in advance the transformation results for a whole catalog. The files can be stored and kept complete in the core memory during execution of the program, so that a search can be accomplished within seconds. 

To code the configuration of a molecule various methods are described in Section 2.8. In particular, the use of wedge symbols clearly demonstrates the value added if stereodescriptors are included in the chemical structure information. The inclusion of stereochemical information gives a more realistic view of the actual spatial arrangement of the atoms of the molecule imder consideration, and can therefore be regarded as between the 2D (topological) and the 3D representation of a chemical structure. 

Tabic 2-6 gives an overview on the most common file formats for chemical structure information and their respective possibilities of representing or coding the constitution, the configuration, i.c., the stereochemistry, and the 3D structure or conformation (see also Sections 2..3 and 2.4). Except for the Z-matrix, all the other file formats in Table 2-6 which are able to code 3D structure information arc using Cartesian coordinates to represent a compound in 3D space. 

JChemPaint is a chemical structure drawing applet. The noteworthy characteristic of this 2D molecule editor is that it is an open source program [208]. This means that the software and the source code of the program are freely available. Every programmer or interested person can participate and enter individual special requests for further development of the application. 

For a review of different coding systems see, for example J.E. Ash, W.A. Warr, P. Willett, Chemical Structure Systems, Ellis Horwood, Chichester, UK, 1991. 

While the trivial and trade nomenclature in most cases has accidental character, the lUPAC Commission has worked out a series of rules [4] which allow the great majority of structures to be represented uniformly, though there still exists some ambiguity within this nomenclature. Thus, many structures can have more than one name. It is important that the rules of some dialects of the lUPAC systematic nomenclature are transformed into a program code. Thus, programs for generating the names from chemical structures, and vice versa (structures from names) have been created [5] (see Chapter II, Section 2 in the Handbook). 

A particularly good selection of physical properties may be spectra, because they are known to depend strongly on the chemical structure. In fact, different types of spectra carry different kinds of structural information, NMR spectra characterize individual carbon atoms in their molecular environment. They therefore correspond quite closely to fragment-based descriptors, as underlined by the success of approaches to predict NMR spectra by fragment codes (see Section 10.2.3). 

To enable the application of electronic data analysis methods, the chemical structures have to be coded as vectors see Chapter 8). Thus, a chemical data set consists of data vectors, where each vector, i.e., each data object, represents one chemical structure. 

The data analysis module of ELECTRAS is twofold. One part was designed for general statistical data analysis of numerical data. The second part offers a module For analyzing chemical data. The difference between the two modules is that the module for mere statistics applies the stati.stical methods or rieural networks directly to the input data while the module for chemical data analysis also contains methods for the calculation ol descriptors for chemical structures (cl. Chapter 8) Descriptors, and thus structure codes, are calculated for the input structures and then the statistical methods and neural networks can be applied to the codes. 

As explained in Chapter 8, descriptors are used to represent a chemical structure and, thus, to provide a coding which allows electronic processing of chemical data. The example given here shows how a GA is used to Rnd an optimal set of descriptors for the task of classification using a Kohoncii neural network. The chromosomes of the GA are to be used as a means for selecting the descriptors they indicate which descriptors are used and which are rejected ... 

The spectral signals are assigned to the HOSE codes that represent the corresponding carbon atom. This approach has been used to create algorithms that allow the automatic creation of "substructure-sub-spectrum databases that are now used in systems for predicting chemical structures directly from NMR. 

We aim to show below how an explicit coding of the chemical structures of the starting materials and products of biochemical reactions and their reaction centers might allow us to achieve progress in our understanding of biochemical pathways. Furthermore, it will be shown how a bridge between chemoinformatics and bioinformatics can be built. 

ChemlDplus at the National Library of Medieine is a database of 56,645 chemical structures. Code of Federal Regulations. 

The numerical solution of the energy balance and momentum balance equations can be combined with flow equations to describe heat transfer and chemical reactions in flow situations. The simulation results can be in various forms numerical, graphical, or pictorial. CFD codes are structured around the numerical algorithms and, to provide easy assess to their solving power, CFD commercial packages incorporate user interfaces to input parameters and observe the results. CFD... 

A non-allergic mechanism imderlying precipitation of asthmatic attacks by aspirin in hypersensitive patients was proposed over 30 years ago [4]. It was founded on pharmacological inhibition of COX of arachidonic acid and explained a cross-reactivity between different NSAIDs varying in chemical structure. This COX theory was confirmed by several studies [11] and was further refined following discovery of the second COX isoenzyme - COX-2. At least two COX isoenzymes, COX-1 and COX-2, are coded by separate genes. Their role in inflammation, asthma and anaphylaxis has been reviewed previously [12]. 

Four main approaches have been suggested for the representation of chemical structures in machine-readable form fragment codes, systematic nomenclature, linear notations, and connection tables. 

ChemIDplus. Published by the U.S. National Library of Medicine, ChemIDplus [62] is a web-based search system, http //chem.sis.nlm.nih.gov/ chemidplus/, that provides free access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. ChemIDplus also provides structure searching and direct links to biomedical resources at NLM and on the Internet. The database contains over 349,000 chemical records, over 56,000 of which include chemical structures, and is searchable by name, synonym, CAS registry number, molecular formula, classification code, locator code, and structure. 

The history and chemistry of the hydroxy-oxime extractants which were originally developed for Cu recovery has been extensively reviewed.11,13,14 Szymanowski s book14 provides comprehensive cover of the literature prior to 1993 and assigns chemical structures to reagents which in most metallurgy texts are referred to only by codes provided by reagent suppliers. An updated version of this information is provided in Table 3. 

RNA RNA (ribonucleic acid) is an information encoded strand of nucleotides, similar to DNA, but with a slightly different chemical structure. In RNA, the letter U (uracil) is substituted for T in the genetic code. RNA delivers DNA s genetic message to the cytoplasm of a cell where proteins are made. 

Fig. 11 (a) Chemical structure left, 9 90°) and cation response right) of virtually decoupled probe 30 for Hg2+ and Ag+. Absorption and emission spectra of 30 in the absence (black, dotted line = fit of the CT emission LE = fluorophore-localized emission band) and presence (at full complexation) of Hg2+ red) and Ag+ blue) in MeCN fluorometric titrations of 1 with Hg2+ and Ag+ shown in the inset FEF (LE) determined from the integrated fluorescence intensity of the LE band, (b) Chemical structures of other virtually decoupled probes for Na+ (31), Pb2+ (32), and Ni2+ (33). For color code, see Fig. 3. (Adapted in part from [115], Copyright 2000 American Chemical Society)...

FIGURE 6.3 Twenty standard amino acids used for cluster analysis of chemical structures. For the three-letter codes, see Table 6.1. 

The many (possibly more than 30) types of collagens found in human connective tissues have substantially the same chemical structure consisting mainly of glycine with smaller amounts of proline and some lysine and alanine. In addition, there are two unusual amino acids, hydroxyproline and hydroxylysine, neither of which has a corresponding base-triplet or codon within the genetic code. There is therefore, extensive post-translational modification of the protein by hydroxylation and also by glycosylation reactions. 

ACC used in the present work was provided by Spectra Corp. (MA, USA) coded as Spectracarb 2225. The chemicals studied catechol and resorcinol were purchased from Sigma and Merck respectively. The chemical structures of these compounds are given in Fig. 21.1. Deionized water was used in adsorption experiments. 

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