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The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR Studies

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Sandia National Laboratories, P.O. Box 969, MS 9951, Livermore, California 94551
Department of Chemical Engineering, Tennessee Technological University, Box 5013, Cookeville, Tennessee 38502
Cite this: J. Chem. Inf. Comput. Sci. 2003, 43, 3, 707–720
Publication Date (Web):March 26, 2003
https://doi.org/10.1021/ci020345w
Copyright © 2003 American Chemical Society
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Abstract

We present a new descriptor named signature based on extended valence sequence. The signature of an atom is a canonical representation of the atom's environment up to a predefined height h. The signature of a molecule is a vector of occurrence numbers of atomic signatures. Two QSAR and QSPR models based on signature are compared with models obtained using popular molecular 2D descriptors taken from a commercially available software (Molconn-Z). One set contains the inhibition concentration at 50% for 121 HIV-1 protease inhibitors, while the second set contains 12865 octanol/water partitioning coefficients (Log P). For both data sets, the models created by signature performed comparable to those from the commercially available descriptors in both correlating the data and in predicting test set values not used in the parametrization. While probing signature's QSAR and QSPR performances, we demonstrates that for any given molecule of diameter D, there is a molecular signature of height h ≤ D+1, from which any 2D descriptor can be computed. As a consequence of this finding any QSAR or QSPR involving 2D descriptors can be replaced with a relationship involving occurrence number of atomic signatures.

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 Corresponding author phone:  (925)294-1279; fax:  (925)294-3020; e-mail:  [email protected]

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