PMID: 9538519Apr 16, 1998Paper

Superposition of three-dimensional chemical structures allowing for conformational flexibility by a hybrid method

Journal of Chemical Information and Computer Sciences
S HandschuhJ Gasteiger

Abstract

The superposition of three-dimensional structures is the first task in the evaluation of the largest common three-dimensional substructure of a set of molecules. This is an important step in the identification of a pharmacophoric pattern for molecules that bind to the same receptor. The superposition method described here combines a genetic algorithm with a numerical optimization method. A major goal is to adequately address the conformational flexibility of ligand molecules. The genetic algorithm optimizes in a nondeterministic process the size and the geometric fit of the substructures. The geometric fit is further improved by changing torsional angles combining the genetic algorithm and the directed tweak method. This directed tweak method is based on a numerical quasi-Newton optimization method. Only one starting conformation per molecule is necessary. Molecules having several rotatable bonds and quite different initial conformations are modified to find large structural similarities. A set of angiotensin II antagonists is investigated to illustrate the performance of the method.

References

Oct 1, 1991·Journal of Computer-aided Molecular Design·C A Pepperrell, P Willett
Mar 1, 1989·Journal of Computer-aided Molecular Design·R A DammkoehlerG R Marshall
Aug 1, 1988·Journal of Chemical Information and Computer Sciences·G M CrippenJ W Peng
Feb 1, 1994·Journal of Computer-aided Molecular Design·G Lauri, P A Bartlett
Feb 2, 1996·Journal of Medicinal Chemistry·R R WexlerP B Timmermans
Dec 1, 1995·Journal of Computer-aided Molecular Design·G JonesR C Glen

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Citations

May 27, 2008·Journal of Molecular Modeling·David T Manallack
Nov 18, 2005·Journal of Computer-aided Molecular Design·Laurence LeherteDaniel P Vercauteren
Oct 13, 2006·Journal of Computer-aided Molecular Design·Nathan BrownJohann Gasteiger
Oct 7, 2009·Journal of Chemical Information and Modeling·Oranit DrorHaim J Wolfson
Aug 2, 2005·Nature Reviews. Drug Discovery·Gisbert Schneider, Uli Fechner
Jun 21, 2002·SAR and QSAR in Environmental Research·J GasteigerL Steinhauer
Feb 14, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Tim HohmDaniel Hoffmann
Apr 22, 2008·Nucleic Acids Research·Dina Schneidman-DuhovnyHaim J Wolfson
Jan 5, 2007·Journal of Computer-aided Molecular Design·Simon J CottrellRobin Taylor
Jul 25, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Leonardo G FerreiraAdriano D Andricopulo
Jun 1, 2012·Expert Opinion on Drug Discovery·Orazio NicolottiAngelo Carotti
May 3, 2007·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Julia HandlJoshua Knowles
May 4, 2005·Journal of Computer-aided Molecular Design·Simon J CottrellDavid J Wilton
May 17, 2010·Molecular Informatics·Sarah R LangdonNathan Brown
Aug 3, 2005·Journal of Computer-aided Molecular Design·Nathan BrownJohann Gasteiger
Dec 15, 2020·Angewandte Chemie·Jie OuyangBenjamin List
Nov 28, 2006·Journal of Chemical Information and Modeling·Martin ReitzJohann Gasteiger
Mar 26, 2003·Journal of Chemical Information and Computer Sciences·Trudi WrightStephen D Pickett
Oct 27, 2006·Journal of Medicinal Chemistry·Johann Gasteiger
Aug 4, 2009·Journal of Chemical Information and Modeling·Whanchul ShinJae Kyung Chon
May 7, 1999·Journal of Medicinal Chemistry·M D MillerS K Kearsley
Sep 2, 2010·Journal of Chemical Information and Modeling·Oliver KorbThomas E Exner
Apr 13, 2000·Journal of Chemical Information and Computer Sciences·X Wang, J T Wang
Mar 26, 2002·Journal of Chemical Information and Computer Sciences·Marc L MansfieldRobert L Jernigan
Mar 26, 2002·Journal of Chemical Information and Computer Sciences·Valerie J GilletDarren V S Green
May 4, 2001·Journal of Medicinal Chemistry·P LabuteJ M Schmidt
May 25, 2004·Journal of Chemical Information and Computer Sciences·Nathan BrownJohann Gasteiger
Jun 13, 2000·Journal of Chemical Information and Computer Sciences·L LeherteD P Vercauteren

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