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| November 22 | ChemAxon launches JChem 3.2 with added .NET compatibility and new GUI's for canonicalization, library enumeration and clustering. |
| October 9 | DeltaSoft's ChemCart to Support ChemAxon's JChem Chemistry Cartridge. Source: DeltaSoft |
| October 3 | ChemAxon Integrates JChem with SciTegic´s Pipeline Pilot - Plugins to be made available for free to the life sciences community |
| September 5 | Evotec acquires global all product ChemAxon license and announces multiple implementations across informatics platform. |
| September 5 | Teijin acquires global structure database management licenses and switches over to JChem platform. |
| August 25 | ChemAxon launches Marvin 4.1 with .NET and publication feature support. |
| June 14 | Archive of the 2006 User Group Meeting posted. |
| May 16 | Aureus Pharma, ChemAxon, Budapest University of Technology and sanofi-aventis Collaborate on European Project related to Toxicity. |
| March 22 | ChemAxon becomes Spotfire Complementary Technology Partner. |
| March 3 | FMC acquires global all product ChemAxon licenses and switches over to JChem structure search platform. |
| Jan 6 | Strand and ChemAxon enter into Collaboration. Source: Strand Life Sciences. |
| Jan 2 | ChemAxon announces free cheminformatics toolkit provision for non-commercial freely accessible web resources. Find out more. |