Chemical cheminformatics

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. 

Chemoinformatics (or cheminformatics) deals with the storage, retrieval, and analysis of chemical and biological data. Specifically, it involves the development and application of software systems for the management of combinatorial chemical projects, rational design of chemical libraries, and analysis of the obtained chemical and biological data. The major research topics of chemoinformatics involve QSAR and diversity analysis. The researchers should address several important issues. First, chemical structures should be characterized by calculable molecular descriptors that provide quantitative representation of chemical structures. Second, special measures should be developed on the basis of these descriptors in order to quantify structural similarities between pairs of molecules. Finally, adequate computational methods should be established for the efficient sampling of the huge combinatorial structural space of chemical libraries. 

This initial medicinal chemistry ELN was followed into the market by products such as the Arthur suite from Synthematix and the iELN system from Intellichem (both since acquired by Symyx), which were more oriented at reaction planning and process chemistry. The heavyweight of the traditional cheminformatics companies, Elsevier MDL, also released a system, called Elan, which combined a Word-based front end with their well-known ISIS chemical technology on the back end (Fig. 9.3). 

In this chapter, we briefly review various aspects of the chemical information systems used by the chemist for literature and patent searches the field of computer-aided drug design technologies, cheminformatics, as well as other applications. We place special emphases on the ligand-based techniques and only briefly mention the structure-based design technologies. 

Xie, P., Muresan, S., Li, J. CLASS - a high-throughput cheminformatic tool for chemical library profiling. Presented at ChemAxon s User Group Meeting 2005, Budapest Hungary, http //www. chemaxon.com/forum / downloads 82.ppt. 

The NIH has set up a consortium called the Molecular Libraries Screening Center Network (MLSCN), which performs HTS on assays provided by the research community. It currently has more than 100,000 chemically diverse compounds. This is an initiative of the Molecular Libraries Roadmap, which also has another two components Cheminformatics and Technology Development. The aim is to generate a comprehensive database of chemical compounds and their bioactivities to enhance the capability for the development of new drug entities. 

In fact, Chemoinformatics is a generic term that encompasses the design, creation, organization, management, retrieval, analysis, dissemination, visualization and use of chemical information. Related terms of chemoinformatics are cheminformatics, chemi-informatics, chemometrics, computational chemistry, chemical informatics, and chemical information management/science. 

The value of the BioPrint dataset is achieved from a combination of high quality in vitro data generated for each compound, and in vivo data extracted from public medical literature (see below). Relating both types of information supports the bioinformatics applications of the database. Also of value is the diversity of compounds, both chemical and biological, which are indicated for a large array of therapeutic areas. This diversity provides a good training set to develop and test various QSAR methods, and supports the cheminformatics applications of the database (Fig. 1). 

Information of our chemical and siRNA libraries is stored in a PostgreSQL database. We annotate our validated hits using a DatabaseReader and a Joiner node to obtain either chemical structures for chemical screens or GenelD for RNAi screens. KNIME has many tools for cheminformatics, can visualize the molecule structures, and has tools to retrieve data from external public databases via Web queries to further annotate hits, allowing clustering either by chemical substructures or GO terms. 

Chemical information systems are complex. This book does not cover every aspect of them. However, it uses a chemical registration system as an example of how to use an object-oriented approach to develop systems in the cheminformatics domain. 

The terms bioinformatics and cheminformatics refer to the use of computational methods in the study of biology and chemistry. Information from DNA or protein sequences, protein structure, and chemical structure is used to build models of biochemical systems or models of the interaction of a biochemical system with a small molecule (e.g., a drug). There are mathematical and statistical methods for analysis, public databases, and literature associated with each of these disciplines. However, there is substantial value in considering the interaction between these areas and in building computational models that integrate data from both sources. In the most... 

Attempts to manage specialized scientific information have given birth to the new discipline of informatics. The branch of informatics that deals primarily with genomic (sequence) data is bioinformatics, whereas cheminformatics deals with chemically oriented data. Informatics examines the way people work with computer-based information. Computers can access huge warehouses of information in the form of databases. Effective mining of these databases can, in principle, lead to knowledge. 

The chemical structure database and registration procedure play dual roles in an enterprise screening informatics environment. These components are essential to the transactional HTS informatics system and serve as the basis for cheminformatics data analysis. While capturing the chemical structures for association with the final screening endpoints, this system also captures and applies the organizational chemical business rules to validate and standardize chemical structures and canonicalize their representations. Structural representation is a critical prerequisite for any subsequent cheminformatics analysis. 

However, given that the cheminformatics and bioinformatics worlds have evolved more or less independently, it is first necessary to establish classification and annotation schemes that link the chemical and biological knowledge spaces. 

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