The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo-and Bioinformatics

By Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, Egon Willighagen. 2003

1,046 citations recorded by the source corpus.

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.

Subfields: Biomedical Engineering, Computational Theory and Mathematics, Materials Chemistry, Computational Chemistry & Drug Discovery

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Citations in the corpus

Interpreting linear support vector machine models with heat map molecule coloring (2011, background): “Explicit hydrogens were added because CDK [21], the core library of the employed fingerprinting algorithms, requires correctly attached hydrogens bonded to an atom.”
Mordred: a molecular descriptor calculator (2018, background): “It is a Python wrapper of numerous other libraries (e.g., Open Babel [16], RDKit [17], Chemistry Development Kit (CDK) [18], Indigo [19], JChem [20], and OPSIN [21]).”
STITCH 4: integration of protein–chemical interactions with user data (2013, methodology): “To avoid biases, we ﬁrst excluded highly similar chemicals, enforcing a maximum Tanimoto similarity of 0.9 (using Algorithm 2 described by Hobohm) (31) using 2D chemical ﬁngerprints calculated with the chemistry development kit (32,33).”
In silico fragmentation for computer assisted identification of metabolite mass spectra (2010, methodology): “Therefore, we cluster the hits with tied ranks using the pairwise Tanimoto [18] distance of the molecular fingerprints, as implemented in the CDK [11].”
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching (2017, methodology): “Previously documented CDK versions have been widely adopted [3, 4].”
Modelling Chemical Reasoning to Predict Reactions (2016, methodology): “37 The ﬁngerprints are then compared by calculating their T ANI - MOTO 6 score T ( A , B ) for continuous values: Chemical Reasoning Algorithm A bi-directional path search is performed as a breadth-ﬁrst search starting from two query molecules M i and M j , see Algorithm 1.”
GPTIPS: An Open Source Genetic Programming Toolbox For Multigene Symbolic Regression (2010, background): “Many of these are commercial products (e.g. DRAGON) but there are also free/open source packages (e.g. the Chemical Descriptors Library (CDL; [9]) and the Chemical Development Kit (CDK; [10]).”
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data (2010, methodology): “…open-source libraries, including JFreeChart (http://www.jfree.org/jfreechart/) for the TIC, spectra, 2D and other visualizers, VisAD (http://www.ssec.wisc.edu/~billh/visad.html) for the 3D visualizer, Chemistry Development Kit (CDK) [12] for calculating isotopic distributions, JChemPaint (http://”