Exploiting Ligand Conformations in Drug Design

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Molecules of the simpUcity of ethane or the complexity of proteins and DNA adopt different conformations. In the case of ethane this gives rise to the notion of a staggered and eclipsed bond, whereas proteins form an array of complex structural elements and DNA - the famous double hehx. The understanding of the conformational properties of small molecules is an important factor in computational approaches contributing to drug discovery. 

This chapter summarizes the computational methodologies used for conformational analysis. Specifically, Section 8.1 gives a theoretical outUne of the problem and presents details of various implementations of computer codes to perform conformational analysis. Section 8.2 describes calculations illustrative of the current accuracy in generating the conformation of a ligand when bound to proteins (the bioactive conformer) by comparisons to crystaUographically observed data. Finally, Section 8.3 concludes by presenting some practical 

Molecular Drug Properties. Measurement and Prediction. R. Mannhold (Ed.) Copyright 2008 Wiley-VCH Verlag GmbH Co. KGaA, Weinheim ISBN 978-3-527-31755-4 

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