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@article{Steinbeck2003,
    abstract = {The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as access information for interested users and potential contributors are given.},
    address = {Max-Planck-Institute of Chemical Ecology, Jena, Germany. c.steinbeck@uni-koeln.de},
    author = {Steinbeck, C. and Han, Y. and Kuhn, S. and Horlacher, O. and Luttmann, E. and Willighagen, E.},
    citeulike-article-id = {423382},
    citeulike-linkout-0 = {http://dx.doi.org/10.1021/ci025584y},
    citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ci025584y},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/12653513},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=12653513},
    doi = {10.1021/ci025584y},
    issn = {0095-2338},
    journal = {J Chem Inf Comput Sci},
    keywords = {cheminformatics, java, opensource, papers},
    number = {2},
    pages = {493--500},
    posted-at = {2007-06-09 09:31:09},
    priority = {0},
    title = {The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics.},
    url = {http://dx.doi.org/10.1021/ci025584y},
    volume = {43},
    year = {2003}
}


@article{Steinbeck2006,
    abstract = {The Chemistry Development Kit (CDK) provides methods for common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Implemented in Java, it is used both for server-side computational services, possibly equipped with a web interface, as well as for applications and client-side applets. This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software.},
    address = {Cologne University Bioinformatics Center (CUBIC), Germany. c.steinbeck@uni-koeln.de},
    author = {Steinbeck, C. and Hoppe, C. and Kuhn, S. and Floris, M. and Guha, R. and Willighagen, E. L.},
    citeulike-article-id = {1073448},
    citeulike-linkout-0 = {http://dx.doi.org/10.2174/138161206777585274},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16796559},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16796559},
    doi = {10.2174/138161206777585274},
    issn = {1381-6128},
    journal = {Current pharmaceutical design},
    keywords = {cheminformatics, java, opensource, papers},
    number = {17},
    pages = {2111--2120},
    posted-at = {2007-06-09 09:28:49},
    priority = {0},
    title = {Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics.},
    url = {http://dx.doi.org/10.2174/138161206777585274},
    volume = {12},
    year = {2006}
}

@article{OBoyle2008,
    abstract = {ABSTRACT: BACKGROUND: Open Source cheminformatics toolkits such as OpenBabel, the CDK and the RDKit share the same core functionality but support different sets of file formats and forcefields, and calculate different fingerprints and descriptors. Despite their complementary features, using these toolkits in the same program is difficult as they are implemented in different languages (C++ versus Java), have different underlying chemical models and have different application programming interfaces (APIs). RESULTS: We describe Cinfony, a Python module that presents a common interface to all three of these toolkits, allowing the user to easily combine methods and results from any of the toolkits. In general, the run time of the Cinfony modules is almost as fast as accessing the underlying toolkits directly from C++ or Java, but Cinfony makes it much easier to carry out common tasks in cheminformatics such as reading file formats and calculating descriptors. CONCLUSION: By providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of OpenBabel, the CDK and the RDKit.},
    author = {O'Boyle, N. M. and Hutchison, G. R.},
    citeulike-article-id = {4277552},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/1752-153X-2-24},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19055766},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19055766},
    doi = {10.1186/1752-153X-2-24},
    issn = {1752-153X},
    journal = {Chemistry Central journal},
    keywords = {cheminformatics, python},
    posted-at = {2009-04-06 08:47:48},
    priority = {2},
    title = {Cinfony - combining Open Source cheminformatics toolkits behind a common interface.},
    url = {http://dx.doi.org/10.1186/1752-153X-2-24},
    volume = {2},
    year = {2008}
}