Cheminformatics chemical space

Wetzel, S., Schuffenhauer, A., Roggo, S., ErtI, P. Vteildmann, H. Cheminformatic analysis of natural products and their chemical space. Chimia 61, 355-360 (2007). 

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. 

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. 

Directly related to the similarity-searching methods are cheminformatics methods that try to align the chemical and biological spaces based on mapping procedures. 

Lastly, while cell-based CSs used in cheminformatic studies are generally partitioned into hypercubes, other possibilities exist that may offer more effective ways to partition these spaces. Rush [160] has mathematically explored some of the possibilities, but practical applications in chemical informatics have not to my knowledge been carried out to date. 

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