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

We compare a range of computational methods for the prediction of sublimation thermodynamics (enthalpy, entropy and free energy of sublimation). These include a model from theoretical chemistry that utilizes crystal lattice energy minimization (with the DMACRYS program) and QSPR models generated by both machine learning (Random Forest and Support Vector Machines) and regression (Partial Least Squares) methods. Using these methods we investigate the predictability of the enthalpy, entropy and free energy of sublimation, with consideration of whether such a method may be able to improve solubility prediction schemes. Previous work has suggested that the major source of error in solubility prediction schemes involving a thermodynamic cycle via the solid state is in the modeling of the free energy change away from the solid state. Yet contrary to this conclusion other work has found that the inclusion of terms such as the enthalpy of sublimation in QSPR methods 2 does not improve the predictions of solubility. We suggest the use of theoretical chemistry terms, detailed explicitly in the methods section, as descriptors for the prediction of the enthalpy and free energy of sublimation. A dataset of 158 molecules with experimental sublimation thermodynamics values and some CSD refcodes has been collected from the literature and is provided with their original source references.

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“…[49][50][51] 132 descriptors were found to contribute information, i.e. their variance was not zero, for the SUB-48 dataset.…”

Section: Cheminformatics Descriptors Sub-48mentioning

confidence: 99%

Are the Sublimation Thermodynamics of Organic Molecules Predictable?

McDonagh

Palmer

Mourik

et al. 2016

J. Chem. Inf. Model.

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“…For the chemoinformatics part, we choose The Chemistry Development Kit (CDK), 11 offering representations of basic chemical concepts such as atoms, bonds, molecules, 2D and 3D structure handling, file input/output for a wide range of formats such as MDL, SMILES, PDB, etc., and a lot of utility functions such as fingerprinting, ring perception, or aromaticity detection.…”

Section: Scopementioning

confidence: 99%

“…The authors would like to thank all members of the CDK project 11 for their contributions, corrections, and helpful comments. Further, our gratitude goes to those who contributed data sets, both via manual input and by providing data sets from in-house collections.…”

Section: Acknowledgmentmentioning

confidence: 99%

NMRShiftDBConstructing a Free Chemical Information System with Open-Source Components

Steinbeck

Krause

Kühn

2003

J. Chem. Inf. Comput. Sci.

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135

140

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The process of designing and implementing NMRShiftDB, an open-source, open-content database for chemical structures and their NMR data based solely on free software is described. NMRShiftDB is available to the community on http://www.nmrshiftdb.org. It allows for open submission and retrieval of data sets by its user community. The software and the content itself is freely distributable, allowing for the establishment of a highly available mirror system of databases in collaborating laboratories.

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“…This has been done for the opensource programs Jmol 21 and JChemPaint 22 via a plugin module interface written as part of the CDK (Chemistry Development Kit). 23,24 This functionalized RSS reader is then rendered capable of parsing the XML and extracting both the DC and e.g. the CML namespaced components for display.…”

Section: Chemical Postprocessing and Aggregation Of Rss Metadatamentioning

confidence: 99%

Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators

Murray‐Rust

Rzepa

Williamson

et al. 2004

J. Chem. Inf. Comput. Sci.

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Examples of the use of the RSS 1.0 (RDF Site Summary) specification together with CML (Chemical Markup Language) to create a metadata based alerting service termed CMLRSS for molecular content are presented. CMLRSS can be viewed either using generic software or with modular opensource chemical viewers and editors enhanced with CMLRSS modules. We discuss the more automated use of CMLRSS as a component of a World Wide Molecular Matrix of semantically rich chemical information.

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

Cited by 245 publications

References 21 publications

Are the Sublimation Thermodynamics of Organic Molecules Predictable?

Are the Sublimation Thermodynamics of Organic Molecules Predictable?

NMRShiftDBConstructing a Free Chemical Information System with Open-Source Components

Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators

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