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Chemoinformatics is a field of solving chemical problems with the application of computational approaches paying particular attention on the manipulation of chemical structural information \cite{Leach_2007} . Greg Paris defines chemoinformatics as “Chemoinformatics is a generic term which encompasses the design, creation, organization, management, retrieval, analysis, dissemination, visualization, and use of chemical information.” The fundamental operations of a chemical information system contain storing, retrieving, and searching information/data and their relationships \cite{Gasteiger_2003}\cite{2003}. Chemoinformatics cover many areas like manipulating of molecular structures, virtual screening, quantitative structure activity relationships (QSAR), de novo design and so on. Open source tools related to two subcategries of QSAR and de nove (ligand) design are defined in own section while the other ones are covered in this section.