Computer-aided molecular design methods

Computer-aided molecular design methods are well suited to modelling reaction pathways, including transition states. These methods can aid significantly not only in the understanding of current catalytic processes but also in the design and identification of new catalysts and even new classes of catalysts. 

Schaeffer H F III (Editor) 1977. Applications of Electronic Structure Theory. New York, Plenum Press. Schaeffer H F III (Editor) 1977. Methods of Electronic Structure Theory. New York, Plenum Press. Stei. art J J P 1990. MOP AC A Semi-Empirical Molecular Orbital Program. Journal of Computer-Aided Molecular Design 4 1-45. 

I J, J C Cole, J P M Lommerse, R S Rowland, R Taylor and M L Verdonk 1997. Isostar A Libraij )f Information about Nonbonded Interactions. Journal of Computer-Aided Molecular Design 11 525-531. g G, W C Guida and W C Still 1989. An Internal Coordinate Monte Carlo Method for Searching lonformational Space. Journal of the American Chemical Scociety 111 4379-4386. leld C and A J Collins 1980. Introduction to Multivariate Analysis. London, Chapman Hall, ig C-W, R M Cooke, A E I Proudfoot and T N C Wells 1995. The Three-dimensional Structure of 1 ANTES. Biochemistry 34 9307-9314. 

Hansson T, J Mturelius and J Aqvist 1998. Ligand Binding Affinity Prediction by Linear InteracHor Energy Methods. Journal of Computer-Aided Molecular Design 12 27-35. 

C and T Lengauer 2000. Computational Methods for the Structural Alignment of Molecules. nal of Computer-Aided Molecular Design 14 215-232. 

Odele, O., and Macchietto, S. (1993). Computer aided molecular design A novel method for optimal solvent selection. Fluid Phase Equilibria, 82,47-54. 

Combinatorial chemistry, 7 380-434 8 400—401 13 283-284. See also High-throughput experimentation applications, 7 381-383 commercial environment, 7 387-389 methodology, 7 383-387 microwaves in, 16 548-552 nomenclature, 7 380 polymers, 7 405—413 Combinatorial libraries, 12 515-517 Combinatorial methods, 7 380 Combinatorial optimization approach, in computer-aided molecular design, 26 1037... 

Boyer, S. and Zamora, I. (2002) New methods in predictive metabolism. Journal of Computer-Aided Molecular Design, 16 (5/6), 403 113. 

This type of solvent selection problem can be formulated and solved as a Computer Aided Molecular Design (CAMD) problem [22], Application of this method for solvent selection and design is highlighted in chapter 14 and is not discussed in detail in this chapter. The ProCAMD software [23], which is based on a hybrid CAMD method can be used to solve solvent selection problems of this type. 

The concepts of molecular similarity (1-3) and molecular diversity (4,5) play important roles in modern approaches to computer-aided molecular design. Molecular similarity provides the simplest, and most widely used, method for virtual screening and underlies the use of clustering methods on chemical databases. Molecular diversity analysis provides a range of tools for exploring the extent to which a set of molecules spans structural space, and underlies many approaches to compound selection and to the design of combinatorial libraries. Many different similarity and diversity methods have been described in the literature, and new methods continue to appear. This raises the question of how one can compare different methods, so as to identify the most appropriate method(s) for some particular application this chapter provides an overview of the ways in which this can be carried out, illustrating such comparisons by,... 

Gaillard, P., Carrupt, P.A., Testa, B. and Boudon, A. (1994) Molecular lipophilicity potential, a tool in 3D-QSAR. Method and applications. Journal of Computer-Aided Molecular Design, 8, 83-96. 

So S-S. and M. Karplus (1999). A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors. Journal of Computer Aided Molecular Design 13 243-258. 

As computers become more pervasive and increasingly powerful, specialized programs and databases are being developed to assist in a wide variety of research efforts. This is true in the search for solvent alternatives, and in this section we review the application of computers to solvent substitution studies and cover computer-aided molecular design of new solvents, methods developed for the prediction of physical properties, methods for predicting less precise chemical characteristics such as toxicity and carcinogenicity, and computer-aided design of alternative synthetic pathways. 

A new method, shape signatures, in the area of computer-aided molecular design has been studied <2003JME5674>. The method has been demonstrated to work well in selecting molecules on the basis of shape and polarity and has been applied to a receptor-based strategy. Dibenzo[ /]thiepine appears in the hit list for 57/-benz[ /]azepin. 

In another example, Chavali et al. demonstrated that 2D connectivity indices can give good structure/property correlations in molybdenum-catalyzed epoxidation [53,54]. They used the Computer Aided Molecular Design (CAMD) environment, a powerful computational tool used in product design. The method uses optimization techniques coupled with molecular design and property estimation methods, generating those molecular structures that match a desired set of properties. 

H. J. Bohm, Prediction of binding constants of protein ligands A fast method for the prioritization of hits obtained from de novo design or 3D database search programs.. Journal of Computer-Aided Molecular Design, 1998, 12, 309-323. 

There are three main classes of methods applicable to product design experimental design, knowledge-based methods, and computer-aided molecular design. 

Journal of Computer Aided Molecular Design. 2001-. Netherlands Kluwer. Monthly. ISSN 0920-654X. URL http //www. kluweronline.com/issn/0920-654X. Computer-based methods in... 

Gonzalez, J. and Ramos de Armas, R. (2002) Markovian chemicals in silico" design (MARCH-INSIDE), a promising approach for computer aided molecular design. II. Experimental and theoretical assessment of a novel method for virtual screening of fasciolicides. J. Mol. Model.,... 

S. K. Kearsley, D. J. Underwood, R. P. Sheridan, and M. D. Miller. Flexibases A way to enhance the use of molecular docking methods. Journal of Computer-Aided Molecular Design, 8 565-582, 1994. 

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