Journal of the Brazilian Chemical Society
Print version ISSN 0103-5053
OPREA, Tudor I.. On the information content of 2D and 3D descriptors for QSAR. J. Braz. Chem. Soc. [online]. 2002, vol.13, n.6, pp. 811-815. ISSN 0103-5053. http://dx.doi.org/10.1590/S0103-50532002000600013.
To gain better understanding on the information content of two-dimensional (2D) vs. three-dimensional (3D) descriptor systems, we analyzed principal component analysis scores derived from 87 2D descriptors and 798 3D (ALMOND) variables on a set of 5998 compounds of medicinal chemistry interest. The information overlap between ALMOND and 2D-based descriptors, as modeled by the fraction of explained variance (r2) and by seven-groups cross-validation (q2) in a two PLS components model was 40%. Individual component analysis indicates that the first and second principal components from the 2D-descriptors are related to the first and third dimensions from the ALMOND PCA model. The first ALMOND component is explained (61%) by size-related descriptors, whereas the third component is marginally explained (25%) by hydrophobicity-related descriptors. Surprisingly, 2D-based hydrogen-bonding descriptors did not contribute significantly in this analysis. These results do not a priori justify the choice of one methodology over the other, when performing QSAR studies.
Keywords : ALMOND; cheminformatics; chemometrics; QSAR.