Chemoinformatics

Chemoinformatics is the application of informatics methods to solve chemical problems. 

Chemoinformatics A Textbook. Edited by Johann Gasteiger and Thomas Engel Copyright 2003 Wiley-VCH Verlag GmbH Co. KGaA. 

The tenn Chemoinformatics appeared only quite recently. Here are some of the first dtings ... 

In this sense, we are rather attached to the broad definition of "Chemoinformatics" ... 

The term has different spellings Chemoinformatics and Cheminformatics. Searches in the database of the Chemical Abstracts Service have shown an approximately equal number of hits for both terms, with Cheminformatics gaining ground somewhat in recent years. Here, we use the spelling "Chemoinformatics" without trying to put forward reasons for that choice. 

Having settled on a definition of chemoinformatics, it is time for us to reflect on the distinction between chemoinformatics and bioinformatics. The objects of interest of bioinformatics are mainly genes and proteins. But genes, DNA and RNA, and proteins are chemical compounds They are objects of high interest in chemistry, Chemists have made substantial contributions to the elucidation of the structure and function of nucleic adds and proteins. The message is dear there is no clearcut distinction between bioinfonnatics and chemoinformatics I... 

Clearly, by tradition, chemoinformatics has largely dealt with small molecules, whereas bioinformatics has started to move from genes to proteins, compounds... 

We will make real progress in understanding the structure, the properties, and the function of proteins, DMA, and RNA only if bioinformatics and chemoinformatics work together ... 

In the case of chemoinformatics this process of abstraction will be performed mostly to gain knowledge about the properties of compounds. Physical, chemical, or biological data of compounds will be associated with each other or with data on the structure of a compound. These pieces of information wQl then be analyzed by inductive learning methods to obtain a model that allows one to make predictions. 

After approaches to the solution of the major tasks in chemoinformatics have thus been outlined, these methods are put to work in specific applications. Some of these apphcations, such as structure elucidation on the basis of spectral information, reaction prediction, computer-assisted synthesis design or drug design, are presented in Chapter 10. 

The field of chemoinformatics was not founded, nor was it formally installed. It slowly evolved from several, often quite humble, begmnings. Scientists in various fields of chemistry struggled to develop computer methods in order to manage the... 

This is not to say that we deem these topics not to be important. On the contrary, we think that those interested in chemoinformatics should strive to obtain a basic knowledge of these subjects. We even think that all professionals in natural sciences and engineering should in future obtain a minimum of training in these fields during their studies. However, presentation here of those aspects of informatics would go beyond the scope of this book. 

Chetnoinformatics has matured to a sdentific discipline that will change - and in some cases has already changed - the way in which we perceive chemistry. The chemical and, in particular, the pharmaceutical industry are in high need of che-moinformatics specialists. Thus, this field has to be taught in academia, both in specialized courses on chemoinformatics and by integrating chemoinformatics into regular chemistry curricula. 

In fact, chemoinformatic curricula have already been initiated at the University of Sheffield, UK, the University of Manchester Institute of Science and Technology, UK, Indiana University, USA, and the Universite de Strasbourg, France. 

In addition to this Textbook, a web page has been estabhshed which provides interesting information including list of URL s and figures (as PDF) to download, and details on chemoinformatics curricula. Moreover, it can also be used as a forum to obtain important information on the book, to find corrections of errors (if any), and to discuss aspects of chemoinformatics. The URL is http //www2. chemie.uni-er an%en.de/puh ications/ci-bQokfindex. html... 

Rings have a profound influence on many properties of a molecule small rings introduce. strain into a molecule, aromatic rings dramatically change its physical and chemical properties, rings present particular problems in syntheses, etc. Thus, a knowledge of the I ings contained in a molecule is important in many applications in chemoinformatics. 

Many organometallic structtircs have chemical bond.s that involve more than two atom centers. This constitutes a major problem for all chemoinformatic systems that do not confine themselves to 3D coordinates. 

Hash coding is an established method in computer science, e.g., in registration procedures [94, 95. In chemoinformatics the structure input occurs as a sequence of characters (names) or numbers (which may also be obtained, e.g., from a connection table (see Section 2.4) by conversion of a structure drawing). Both names and numbers may be quite large and may not be usable as an address... 

In chemoinformatics, chirality is taken into account by many structural representation schemes, in order that a specific enantiomer can be imambiguously specified. A challenging task is the automatic detection of chirality in a molecular structure, which was solved for the case of chiral atoms, but not for chirality arising from other stereogenic units. Beyond labeling, quantitative descriptors of molecular chirahty are required for the prediction of chiral properties such as biological activity or enantioselectivity in chemical reactions) from the molecular structure. These descriptors, and how chemoinformatics can be used to automatically detect, specify, and represent molecular chirality, are described in more detail in Chapter 8. 

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... 

The JME Editor is a Java program which allows one to draw, edit, and display molecules and reactions directly within a web page and may also be used as an application in a stand-alone mode. The editor was originally developed for use in an in-house web-based chemoinformatics system but because of many requests it was released to the public. The JME currently is probably the most popular molecule entry system written in Java. Internet sites that use the JME applet include several structure databases, property prediction services, various chemoinformatics tools (such as for generation of 3D structures or molecular orbital visualization), and interactive sites focused on chemistry education [209]. 

Inf Comput. Sd. 1995, 35, 663-674. p08] [. Aires-de-Sousa, Representation of molecular chirality, in Handbook of Chemoinformatics, J. Gasteiger (Ed.) Xaiey-VCH, Weinheim, Chapter VIII, Section 4. 

Soc. 1974, 96, 4S34--i842. pi3] D. Weininger, SMILES - a language for molecules and reactions, in Handbook of Chemoinformatics, J. Gasteiger (Ed.) Wiley-VCH, Weinheim, 2003, Chapter 11, Section 3. pi4] G. M. Crippen, T.F. Havel, Distance geometry and molecular conformations, in Chemometrics Research Studies Series 15 D. Bawden (Ed.), Research Studies Press (Wiley), New York, 1988. 

The objective of chemoinformatics is to assist the chemist in giving access to reaction information, in deriving knowledge on chemical reactions, in predicting the course and outcome of chemical reactions, and in designing syntheses. Specifically, the problems of accomplishing the following tasks have to be solved ... 

The major task of chemoinformatics is to find these relationships between the data on the molecular structure and the data on the physical, chemical, or biological properties of the molecules. 

Returning to datasets from chemoinformatics, we may conclude that the first case stands for the complete degeneracy of the dataset, when all but one data object are redimdant. The second case corresponds to the weird situation in which all the objects of the dataset are outliers. We have thus arrived at the extreme extents of the dataset complexity. 

Similarity searching is the database implementation of the similarity concept. Some of the steps involved in similarity searching are overviewed next, in the context of chemoinformatics. 

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