An alignment-independent versatile structure descriptor for QSAR and QSPR based on the distribution of molecular features

A molecular descriptor based upon a count statistic of the topological distance matrix is described and evaluated for use in QSAR studies. Encoding a molecule is done by computing many selective count statistics (histograms) reflecting the distribution of different atom types and bond types in the molecule. The descriptor was also extended to incorporate geometric features of molecules by weighting the topological distance counts with the geometric distance. It is invariant to both translation and rotation. As a result, it does not require the alignment of the structures under study. The method was applied to several QSAR data sets and performed equally well or better than CoMFA and the EVA descriptor. Compared to the latter two methods, it is computationally easier.