The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies

Journal of Chemical Information and Computer Sciences
Jean-Loup FaulonRamdas S Pophale

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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Citations

Dec 21, 2005·Journal of Molecular Modeling·W Michael BrownJean-Loup Faulon
Nov 4, 2005·Journal of Computer-aided Molecular Design·Jean-Loup FaulonShawn Martin
Nov 18, 2005·Journal of Computer-aided Molecular Design·A VarnekV P Solov'ev
Oct 12, 2012·Journal of Computer-aided Molecular Design·Peter Ertl, Richard Lewis
Jun 5, 2004·Journal of Molecular Graphics & Modelling·Carla J ChurchwellJean-Loup Faulon
Jun 20, 2002·Journal of Molecular Graphics & Modelling·Donald P ViscoJean-Loup Faulon
Jul 22, 2011·Journal of Chemical Information and Modeling·Ola SpjuthLars Carlsson
Aug 17, 2012·Journal of Chemical Information and Modeling·Aurélie de LucaAlexandre Varnek
Jun 5, 2012·Journal of Chemical Information and Modeling·Shawn Martin
Jun 26, 2013·Journal of Chemical Information and Modeling·Hongming ChenIngemar Nilsson
Nov 30, 2013·Nature Reviews. Drug Discovery·John G CummingHongming Chen
Aug 21, 2004·Bioinformatics·Shawn MartinJean-Loup Faulon
Jun 7, 2013·Bioinformatics·Michal RostkowskiPatrik Rydberg
May 23, 2012·BMC Bioinformatics·Kalai Vanii JayaseelanChristoph Steinbeck
Feb 10, 2010·Journal of Cheminformatics·William Wl Wong, Forbes J Burkowski
Oct 8, 2008·Journal of Molecular Graphics & Modelling·Eckart BindewaldBruce A Shapiro
Oct 22, 2016·ACS Synthetic Biology·Vincent LibisJean-Loup Faulon
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Apr 8, 2014·Journal of Biotechnology·Alfred Fernández-CastanéJean-Loup Faulon
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