PMID: 11606120Oct 19, 2001Paper

Measuring molecular similarity and diversity: total pharmacophore diversity

Journal of Medicinal Chemistry
G M Makara

Abstract

A novel method, total pharmacophore diversity (ToPD), based on known pharmacophore features for numerically defining molecular similarity or diversity is described. The method captures the 3D shape and functionality of molecules by the analysis of relevant intramolecular distances to generate a short and descriptive pharmacophoric fingerprint for each molecule. The ToPD fingerprints can then be used in diversity analysis, clustering, or database searching. Conformational sampling is carried out when needed by the means of molecular dynamics. Our results show that ToPD outperforms a traditional 2D fingerprint technique in all test cases.

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Citations

Oct 16, 2003·Current Opinion in Pharmacology·Michael Williams
Jan 28, 2003·Drug Discovery Today·Robert P Sheridan, Simon K Kearsley
Aug 21, 2003·Drug Discovery Today·Giang Thanh LeWim Meutermans
Mar 4, 2006·SAR and QSAR in Environmental Research·A G MaldonadoB T Fan
Nov 9, 2012·Journal of Cheminformatics·Sunghwan KimStephen H Bryant
Nov 30, 2006·Drug Discovery Today·Peter Willett
Nov 24, 2004·Journal of Chemical Information and Computer Sciences·Nicolas BaurinRoderick E Hubbard
Mar 26, 2003·Journal of Chemical Information and Computer Sciences·Ansgar SchuffenhauerEdgar Jacoby
Jan 13, 2006·Molecular Diversity·Ana G MaldonadoBo-Tao Fan
Apr 9, 2008·Journal of Chemical Information and Modeling·Modest von KorffThomas Sander
Jun 15, 2007·Journal of Medicinal Chemistry·Gergely M Makara
Nov 30, 2004·Journal of Medicinal Chemistry·Jeremy L JenkinsJohn W Davies
Jul 25, 2006·Journal of Chemical Information and Modeling·Sara H FitzgeraldH Mario Geysen
Jul 25, 2006·Journal of Chemical Information and Modeling·Elisabet Gregori-Puigjané, Jordi Mestres
Jul 25, 2006·Journal of Chemical Information and Modeling·Rajarshi GuhaTing Chen
Sep 6, 2002·Journal of Medicinal Chemistry·Yvonne C MartinLinda M Traphagen
Dec 13, 2006·Journal of Medicinal Chemistry·James H NettlesMeir Glick

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