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Ambit \cite{Jeliazkova_2011} integrates with CDK to provide web-based applications for chemical search and analysis.  Bioclipse \cite{Spjuth_2009}  is a workbench, based on the Eclipse framework, for manipulating and analyzing biochemical data and databases. It integrates with CDK and Jmol to provide cheminformatic functionality and also has modules for bioinformatics (primarly sequence analysis) and QSAR modeling. \paragraph{Conformer Generation} \paragraph{Other}