PMID: 11911709Mar 26, 2002Paper

On combining recursive partitioning and simulated annealing to detect groups of biologically active compounds

Journal of Chemical Information and Computer Sciences
P E BlowerJeffrey Bjoraker

Abstract

Statistical data mining methods have proven to be powerful tools for investigating correlations between molecular structure and biological activity. Recursive partitioning (RP), in particular, offers several advantages in mining large, diverse data sets resulting from high throughput screening. When used with binary molecular descriptors, the standard implementation of RP splits on single descriptors. We use simulated annealing (SA) to find combinations of molecular descriptors whose simultaneous presence best separates off the most active, chemically similar group of compounds. The search is incorporated into a recursive partitioning design to produce a regression tree for biological activity on the space of structural fingerprints. Each node is characterized by a specific combination of structural features, and the terminal nodes with high average activities correspond, roughly, to different classes of compounds. Using LeadScope structural features as descriptors to mine a database from the National Cancer Institute, the merging of RP and SA consistently identifies structurally homogeneous classes of highly potent anticancer agents.

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Citations

Feb 26, 2005·Journal of Computer-aided Molecular Design·Nadège PiclinJacques R Chrétien
Jun 25, 2008·Journal of Computer-aided Molecular Design·Haiyan LiZhonggui He
Jul 10, 2003·Drug Discovery Today·Cédric MerlotDennis J Church
Feb 18, 2016·Regulatory Toxicology and Pharmacology : RTP·Ernst AhlbergGlenn J Myatt
Jun 12, 2014·Chemical Biology & Drug Design·Rohit R JoshiEvans C Coutinho
May 11, 2010·European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences·Taravat Ghafourian, Atefeh Haji Agha Bozorgi
Dec 1, 2004·Drug Discovery Today. Technologies·Karl-Heinz Baringhaus, Gerhard Hessler
Jun 9, 2004·Current Opinion in Chemical Biology·Daniel C Weaver
Feb 2, 2012·The Journal of Toxicological Sciences·Haslan RoslieSalmaan Hussain Inayat-Hussain
Sep 27, 2005·Drug Discovery Today·Peter W Swaan, Sean Ekins
Jul 24, 2013·Technometrics : a Journal of Statistics for the Physical, Chemical, and Engineering Sciences·Ke ZhangS Stanley Young
Nov 5, 2002·Nature Reviews. Drug Discovery·Jürgen Bajorath
Apr 23, 2005·SAR and QSAR in Environmental Research·T Ghafourian, M T D Cronin
Mar 26, 2003·Journal of Chemical Information and Computer Sciences·Edward J BarkerJeff Morris
Mar 26, 2003·Journal of Chemical Information and Computer Sciences·Weida TongRoger Perkins
Mar 26, 2003·Journal of Chemical Information and Computer Sciences·David W Miller
May 22, 2007·Journal of Chemical Information and Modeling·Dimitris K AgrafiotisHerman van Vlijmen
Jun 8, 2010·Journal of Medicinal Chemistry·Dimitris K Agrafiotis, John J M Wiener
Jan 28, 2003·Journal of Chemical Information and Computer Sciences·Jeffrey W GoddenJürgen Bajorath
Oct 17, 2003·Journal of Medicinal Chemistry·Kevin P CrossPaul E Blower
Nov 25, 2003·Journal of Chemical Information and Computer Sciences·Jeffrey J SutherlandDonald F Weaver
May 23, 2006·Journal of Chemical Information and Modeling·Ramaswamy NilakantanDominick Mobilio
May 25, 2004·Journal of Chemical Information and Computer Sciences·Robert Kirk DeLisle, Steven L Dixon
May 28, 2003·Journal of Chemical Information and Computer Sciences·Jeffrey J Sutherland, Donald F Weaver

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