Journal ArticleDOI
The Chemistry Development Kit (CDK): An Open‐Source Java Library for Chemo‐ and Bioinformatics.
Christoph Steinbeck,Yongquan Han,Stefan Kuhn,Oliver Horlacher,Edgar Luttmann,Egon Willighagen +5 more
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TLDR
The Chemistry Development Kit (CDK) as mentioned in this paper is an open-source Java library for Structural Chemo- and Bioinformatics that provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures.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.read more
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The Blue Obelisk—Interoperability in Chemical Informatics
Rajarshi Guha,Michael T. Howard,Geoffrey R. Hutchison,Peter Murray-Rust,Henry Rzepa,Christoph Steinbeck,Jörg K. Wegner,Egon Willighagen +7 more
TL;DR: The Blue Obelisk Movement is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards.
Journal ArticleDOI
HAPPI: an online database of comprehensive human annotated and predicted protein interactions
TL;DR: HAPPI is by far the most comprehensive public compilation of human protein interaction information and enables its users to fully explore PPI data with quality measures and annotated information necessary for emerging network biology studies.
Journal ArticleDOI
Fragmentation trees reloaded
Sebastian Böcker,Kai Dührkop +1 more
TL;DR: SIRIUS 3 can be a part of an untargeted metabolomics workflow, allowing researchers to investigate unknowns using automated computational methods, and demonstrates the superiority of the new scoring for two tasks.
Journal ArticleDOI
Observing local and global properties of metabolic pathways
TL;DR: A new method to rank the enzymes/metabolites in the metabolic network and a model to determine and rank the biochemical lethality in metabolic networks (enzymes/ metabolites) through 'choke points' are demonstrated.
Journal ArticleDOI
A generalizable definition of chemical similarity for read-across
Matteo Floris,Alberto Manganaro,Orazio Nicolotti,Ricardo Medda,Giuseppe Felice Mangiatordi,Emilio Benfenati +5 more
TL;DR: The comparison of multiple combinations of binary fingerprints and similarity metrics for computing the chemical similarity in the context of two different applications of the read-across technique demonstrates that the classical similarity measurements can be improved with a generalizable model of similarity.
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Journal ArticleDOI
The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics
Christoph Steinbeck,Yongquan Han,Stefan Kuhn,Oliver Horlacher,Edgar Luttmann,Egon Willighagen +5 more
TL;DR: The Chemistry Development Kit 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.