Combinatorial rational design

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. 

W Zheng, SI Cho, A Tropsha. Rational combinatorial library design 1. Focus-2D A new approach to the design of targeted combinatorial chemical libraries. J Chem Inf Comput Sci 38 251-258, 1998. 

Rohlin, L., Oh, M.K., and Liao, J.C., Microbial pathway engineering for industrial processes evolution, combinatorial biosynthesis and rational design, Curr. Opin. Microbiol. 4, 330, 2001. 

Plants are combinatorial chemists par excellence, and understanding the principles that relate enzyme structure to function will open up unlimited possibilities for the rational design of new enzymes to generate novel biologically active natural products (see Chapter by Noel et al.). 

Potyrailo, R. A., Polymeric sensor materials Toward an alliance of combinatorial and rational design tools , Angew. Chem. Int. Ed. 2006, 45, 702 723... 

Savchuk, N.P., Tkachenko, S.E., and Baiakin, K.V. Rational design of GPCR-specific combinatorial libraries based on the concept of privileged substructures. In Chemoinformatics in... 

Zheng, W., Cho, S.J., and Tropsha, A. Rational combinatorial library design. 

Teopsha, a., Cho, S.)., Zheng, W. New Tricks for an Old Dog development and application of novel QSAR methods for rational design of combinatorial chemical libraries and database mining. In Rational Drug Design Novel Methodology and Practical Applications, ACS Symposium Series Vol. 719, Paeeill,... 

Cho, S.J., Zheng, W., Teopsha, A. Rational combinatorial library design. 2. Rational design of targeted combinatorial peptide libraries using chemical similarity probe and the inverse QSAR approaches./. Chem. Inf. Comput. Sci. 1998, 38, 259-268. 

Nielsen, M. C. Ulven, T. Selective extraction of G-quadruplex ligands from a rationally designed scaffold-based dynamic combinatorial library. Chem. Ear. J. 2008,14, 9487-9490. 

Tropsha, A., Zheng, W., and Cho, S. J. (1996) Application of topological indices in rational design of combinatorial chemical libraries. Book of Abstracts, 211th ACS National Meeting, New Orleans, LA, March 22-28, American Chemical Society Washington, DC. 

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