PMID: 11604039Oct 18, 2001Paper

Estimation of molecular similarity based on 4D-QSAR analysis: formalism and validation

Journal of Chemical Information and Computer Sciences
J S Duca, A J Hopfinger

Abstract

The 4D-QSAR paradigm has been used to develop a formalism to estimate molecular similarity measures as a function of conformation, alignment, and atom type. It is possible to estimate the molecular similarity of pairs of molecules based upon the entire ensemble of conformational states each molecule can adopt at a given temperature, normally room temperature. Molecular similarity can be measured in terms of the types of atoms composing each molecule leading to multiple measures of molecular similarity. Multiple measures of molecular similarity can also arise from using different alignment rules to perform relative molecular similarity, RMS, analysis. An alignment independent method of determining molecular similarity measures, referred to as absolute molecular similarity, AMS, analysis has been developed. Various sets and libraries of compounds, including the amino acids, are analyzed using 4D-QSAR molecular similarity analysis to demonstrate the features of the formalism. Exploration of molecular similarity as a function of chirality, identification of common embedded 3D pharmacophores in compounds, and elucidation of 3D-isosteric compounds from structurally diverse libraries are carried out in the application studies.

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Citations

Feb 25, 2011·Molecular Diversity·Daniel J Graham, Jessica L Greminger
Sep 6, 2005·IEEE Transactions on Visualization and Computer Graphics·Purvi SaraiyaKaren Duca
Apr 24, 2014·Journal of Biomolecular Structure & Dynamics·Vijay M KhedkarEvans C Coutinho
Nov 10, 2010·The Science of the Total Environment·Izacar MartínezRobert Rallo
Jul 26, 2018·SAR and QSAR in Environmental Research·I Luque Ruiz, M Á Gómez-Nieto
Nov 5, 2002·Nature Reviews. Drug Discovery·Jürgen Bajorath
Mar 9, 2018·SAR and QSAR in Environmental Research·I Luque Ruiz, M Á Gómez-Nieto
Jul 27, 2010·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Carolina H AndradeAnton J Hopfinger
May 11, 2019·Current Topics in Medicinal Chemistry·Oscar Martínez-SantiagoHai Pham-The
Mar 24, 2011·Future Medicinal Chemistry·Chenzhong Liao, Marc C Nicklaus
Dec 10, 2009·Journal of Chemical Information and Modeling·Jitender VermaEvans Coutinho
Jun 3, 2021·International Journal of Molecular Sciences·Andrzej Bak
Dec 24, 2014·Journal of Chemical Information and Modeling·Vijay M Khedkar, Evans C Coutinho
Oct 27, 2017·Journal of Chemical Information and Modeling·Irene Luque Ruiz, Miguel Ángel Gómez-Nieto
May 16, 2012·Journal of Chemical Information and Modeling·Alexandre Varnek, Igor Baskin
Sep 18, 2021·SAR and QSAR in Environmental Research·K SahinS Durdagi

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