The Influence of Structure Representation on QSAR Modelling
In all kinds of QSAR studies it is very important how the chemical structure is represented. Usually a set of structural properties, calculated or extracted experimentally, is considered as a structure representation vector when compared and correlated to a biological property. Numerous attempts to suggest different structure representations reflect the vital importance of the structural coding problem in all kind of modelling procedures. Just a few examples are given for illustration in references1–7. One possible way of representing structures is by using a complete 3D structure information — atom type and coordinates. However, this representation suffers primarily from the lack of uniformity. Molecules containing different number of atoms N yield representations of matrices of various size (N×3 or N×4). Molecular descriptors originating from graph theory overcome the uniformity problem, they are also suitable because of their simplicity and often show good correlation with molecular properties8 but the 3-D structural properties of compounds are lost. With the new “spectrum-like” structure code developed by Zupan et al.6,7 the 3D representation is uniform, unique and reversible.
KeywordsMultiple Linear Regression Structure Representation Multiple Linear Regression Model Molecular Descriptor Mulliken Charge
Unable to display preview. Download preview PDF.
- 6.M. Novič, J. Zupan, A New General and Uniform Structure Representation, Software-Entwicklung in der Chemie 10, Johann Gasteiger (Ed.), Frankfurt am Main, pg. 47–58, (1996).Google Scholar
- 8.M. Randić, M. Razinger, On characterization of 3D molecular structure, in: From Chemical Topology to Three-Dimensional Geometry ( A. T. Balaban, Ed.), Plenum Press, New York, (1997).Google Scholar
- 9.A. R. Katritzky, V. S. Lobanov, M. Karelson, CODESSA 2.0, Comprehensive Descriptors for Structural and Statistical Analysis, Copyright (c) 1994–1996 University of Florida, U.S.A.Google Scholar
- 10.D.L. Massart, B.G. M. Vandengiste, S.N. Deming, Y. Michotte and L. Kaufman, Chemometrics: a textbook, Elsevier, Amsterdam, (1988).Google Scholar