Cheminformatics

Clustering by 2D fingerprints is a very common procedure, and yet there are still many unanswered questions, principally aroimd the choice of descriptor, and the selection of a statistically appropriate number of clusters. Wild and Blankley have looked at these issues and have come to some interesting conclusions MACCS-like keys are best for general diverse sets (e.g. corporate databases), whereas Daylight-like keys are the best for similar sets (e.g. combinatorial libraries) the best method for eluster-level selection is dataset-dependent. However, the Kelley method seems to have the best worst-case performance across the different datasets and deseriptors. Xue et al. have developed a method for using consensus 

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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. 

The life sciences domain task force (LSR DTP) has several working groups architecture and road map, biochemical pathways, cheminformatics, gene expression, sequence analysis, and single nucleotide polymorphisms. 

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). 

More can be found at http //www.bioinformatics.org, http //www.open-bio.org, http //www.cheminformatics.org, and http //www.chemoinf.com. 

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. 

We have been developing cutting-edge data analysis tools for the pharmaceutical industry for over a decade, with a particular focus in the fields of cheminformatics and bioinformatics. We now describe how our insights apply to these areas. 

We have worked in the field of cheminformatics for about a decade, and in particular we have developed statistical and computer science technology for sequential screening and advocated a paradigm shift to its adoption within the pharmaceutical and biotechnology industries (see Fig. 17.2). 

Let us examine cheminformatics technologies with our four questions ... 

Anari MR, Baillie TA. Bridging cheminformatic metabolite prediction and tandem mass spectrometry. Drug Discov Today 2005 10 711-7. 

Colmenarejo G, Alvarez-Pedraglio A and Lavandera JL. Cheminformatic models to predict binding affinities to human serum albumin. J Med Chem 2001 44 4370-8. 

Weifan Zheng, Cheminformatics Research Resources, Division of Medicinal Chemistry, School of Pharmacy, University of North Carolina at Chapel Hill, NC 27599-7360, USA. (weifan zheng unc.edu). 

Erd, P., Mtihlbacher, J. Rohde, B., Selzer, P. Web-based cheminformatics and molecular property prediction tools supporting drug design and development at Novartis. SAR QSAR Environ. Res. 2003, 34, 321-328. 

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. 

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