Comparative field analysis

Klebe G, Abraham U (1993) On the prediction of binding properties of dmg molecules by comparative field analysis. J Med Chem 36 70-80... 

Before the comparative molecular field analysis (CoMFA), BCUT descriptors, 4D-QSAR, and HYBOT descriptors arc discussed in more detail, some further descriptors are listed briefly. 

After an alignment of a set of molecules known to bind to the same receptor a comparative molecular field analysis CoMFA) makes it possible to determine and visuahze molecular interaction regions involved in hgand-receptor binding [51]. Further on, statistical methods such as partial least squares regression PLS) are applied to search for a correlation between CoMFA descriptors and biological activity. The CoMFA descriptors have been one of the most widely used set of descriptors. However, their apex has been reached. 

Cramer R D III, D E Patterson and J D Bunce 1988, Comparative Molecular Field Analysis (CoMFA). Effect of Shape on Binding of Steroids to Carrier Proteins. Journal of the American Chemical Societ 110 5959-5967. 

Poso A, R Juvonen and J Gynther 1995. Comparative Molecular Field Analysis of Compounds wii CYP2A5 Binding Affinity. Quantitative Structure-Activity Relationships 14 507-511. 

RD Cramer III, DE Patterson, JD Bunce. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc 110 5959-5967, 1988. 

Bis(oxazohnes) figands have been so widely used for the Diels-Alder reaction between N-2-alkenoyl-l,3-oxazolidine-2-one and cyclopentadiene that Lipkowitz and Pradhan developed a QSAR (quantitative structure-activity relationship) using Comparative Molecular Field Analysis (CoMFA) for a set of 23 copper-catalysts containing mainly bis(oxazoline) figands. The generated... 

Cho SJ, Tropsha A. Cross-validated R2-Guided region selection for comparative molecular field analysis a simple method to achieve consistent results. I Med Chem 1995 38(7) 1060-6. 

Asikainen A, Tarhanen J, Poso A, Pasanen M, Alhava E, Jnvonen RO. Predictive valne of comparative molecular field analysis modelling of naphthalene inhibition of human CYP2A6 and mouse CYP2A5 enzymes. Toxicol In Vitro 2003 17 449-55. 

A widely used 3-D QSAR method that makes use of PLS is comparative molecular field analysis (CoMFA), in which a probe atom is used to calculate the steric and electronic fields at numerous points in a 3D lattice within which the molecules have been aligned. Poso et al. [56] used the technique to model the binding of coumarins to cytochrome P450 2A5, with similar results to those obtained by Bravi and Wikel [55]. Shi et al. [57] used it to model the estrogen receptor binding of a large diverse set of compounds, and Cavalli et al. [58] used it to develop a pharmacophore for hERG potassium... 

Poso A, luvonen R, Gynther I. Comparative molecular field analysis of compounds with CYP2A5 binding affinity. Quant Struct-Act Relat 1995 14 507-11. 

Swaan PW, Szoka FC, Jr. and Oie S. Molecular modeling of the intestinal bile acid carrier a comparative molecular field analysis study. J Comput Aided Mol Des 1997 11 581-8. 

Kim, K. H. Calculation of hydrophobic parameters directly from three-dimensional structures using comparative molecular field analysis. J. Comput.-Aided Mol. Des. 1995, 9,... 

Partial Least Squares (PLS) regression (Section 35.7) is one of the more recent advances in QSAR which has led to the now widely accepted method of Comparative Molecular Field Analysis (CoMFA). This method makes use of local physicochemical properties such as charge, potential and steric fields that can be determined on a three-dimensional grid that is laid over the chemical stmctures. The determination of steric conformation, by means of X-ray crystallography or NMR spectroscopy, and the quantum mechanical calculation of charge and potential fields are now performed routinely on medium-sized molecules [10]. Modem optimization and prediction techniques such as neural networks (Chapter 44) also have found their way into QSAR. 

J. W. McFarland, Comparative Molecular Field Analysis (CoMFA) of anticoccidial triazines. J. Med. Chem., 35 (1992) 2543-2550. 

To refine this model qualitatively, the binding of several of these compounds was subjected to a CoMFA (Comparative Molecular Field Analysis) [39], This program examines electrostatic and steric parameters... 

E. E., Tukker, J. J., Mapping the binding site of the small intestinal peptide carrier (PepTl) using comparative molecular field analysis, Receptors Channels 1998, 6, 189-200. 

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