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OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data

Anthony R. Bradley, Ian D. Wall, Darren V. S. Green, Charlotte M. Deane, Brian D. Marsden
2014 Journal of Chemical Information and Modeling  
In this paper we describe OOMMPPAA, a novel computational tool designed to inform compound design by combining such data. OOMMPPAA uses 3D matched molecular pairs to generate 3D ligand conformations.  ...  We present validation of the tool using openly available data for CDK2 and a GlaxoSmithKline data set for a SAM-dependent methyl-transferase.  ...  Notes The authors declare no competing financial interest. ■ ACKNOWLEDGMENTS We would like to thank Stephen Pickett and Jameed Hussain for useful discussions of the method.  ... 
doi:10.1021/ci500245d pmid:25244105 pmcid:PMC4372120 fatcat:jmzgroigvrgkxmbr67nwohe7c4

Automatic Identification of Analogue Series form Large Compound Data Sets: Methods and Applications

José Naveja, Martin Vogt
2021 Molecules  
These methods enable the efficient analysis of large data sets with hundreds of thousands or even millions of compounds and have spawned many related methodological developments.  ...  Later on, the matched molecular pair concept led to efficient algorithms to identify similar compounds sharing a common core structure by exploring many putative scaffolds for each compound.  ...  For example, in Reference [60] , the directed R-group combination graph represents R-groups tables in a directed graph structure, based on the substituents for each analogue.  ... 
doi:10.3390/molecules26175291 pmid:34500724 pmcid:PMC8433811 fatcat:wu6mnku37zb7fo2jz64viatf3u