{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2007/07/14/cdk-literature-2.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/17nhx-htt54", "url": "https://chem-bla-ics.linkedchemistry.info/2007/07/14/cdk-literature-2.html", "title": "CDK Literature #2", "content_html": "

Second in a series of articles summarizing articles that cite one of the main CDK articles for\nCDK News. The first CDK Literature \nwas already half a year ago, so it was about time.

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Bioclipse

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Nothing much I have to say about that. Just browse my blog and\nyou’ll see that it heavily uses CDK, JChemPaint and Jmol. See also the Bioclipse blog.
\nOla Spjuth, Tobias Helmus, Egon Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust,\nChristoph Steinbeck, Jarl Wikberg, Bioclipse: an open source workbench for chemo- and bioinformatics, BMC Bioinformatics,\n2007, 8(59), doi:10.1186/1471-2105-8-59

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Proteomics in 2005/2006

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Review article on proteomics which mentions the CDK and JChemPaint in the data analysis section, but it does not cite them.\nIt does cite the Bioclipse article though.
\nJeffrey Smith, Jean-Philippe Lambert, Fred Elisma, Daniel Figeys, Proteomics in 2005/2006: Developments, applications\nand challenges, Analytical Chemistry, 2007, 79(12):4325-4343, doi:10.1021/ac070741j

\n\n

Combinatorial Enumeration

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Article by Andreas on SmiLib (BSD-like license) which\nis library for combinatorial enumeration using building blocks. The CDK is used for the addition of explicit\nhydrogens and the creation of MDL SD files. Andreas mentions in the article that the CDK’s SMILES parser ignores\nstereo chemistry.
\nAndreas Schüller, Volker Hänke, Gisbert Schneider, SmiLib v2.0: A Java-Based Tool for Rapid Combinatorial Library\nEnumeration, QSAR & Combinatorial Science, 2007, 26(3):407-410, doi:10.1002/qsar.200630101

\n\n

Molecular Query Language

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This article is also from the group of Gisbert. Ewgenij introduces an open standard SMARTS replacement, covered in\nCDK News in 2005 . There is an interface to the CDK, but the\nlicense of the reference implementation makes it impossible to distribute it with the CDK itself. This is rather\nunfortunate, because if it would have been possible, a number of implementations in the CDK, such as atom type\nperception, could be based on MQL. See also Jörgs blog on MQL.
\nEwgenij Proschak, Jörg Wegner, Andreas Schüller, Gisbert Schneider, Uli Fechner, J. Chem. Inf. Model., 2007, 47(2):295-301,\ndoi:10.1021/ci600305h

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Golden Rules in Mass Spectroscopy

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Tobias Kind wrote about structure elucidation using mass spectra, and discusses MolGen and CDK’s DeterministicStructureGenerator,\nand mentions problems with both generators. He has been in contact with the CDK and recently did\nextensive tests.
\nTobias Kind and Oliver Fiehn, Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass\nspectrometry, BMC Bioinformatics, 2007, 8:105, doi:10.1186/1471-2105-8-105

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References

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Kind, T., & Fiehn, O. (2007). Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics, 8(1). https://doi.org/10.1186/1471-2105-8-105 CrossRef Scholia
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Proschak, E., Wegner, J. K., Schüller, A., Schneider, G., & Fechner, U. (2007). Molecular Query Language (MQL)A Context-Free Grammar for Substructure Matching. Journal of Chemical Information and Modeling, 47(2), 295–301. https://doi.org/10.1021/ci600305h CrossRef Scholia
\n
Schüller, A., Hähnke, V., & Schneider, G. (2007). SmiLib v2.0: A Java‐Based Tool for Rapid Combinatorial Library Enumeration. QSAR & Combinatorial Science, 26(3), 407–410. https://doi.org/10.1002/qsar.200630101 CrossRef Scholia
\n
Smith, J. C., Lambert, J.-P., Elisma, F., & Figeys, D. (2007). Proteomics in 2005/2006:  Developments, Applications and Challenges. Analytical Chemistry, 79(12), 4325–4344. https://doi.org/10.1021/ac070741j CrossRef Scholia
\n
Spjuth, O., Helmus, T., Willighagen, E. L., Kuhn, S., Eklund, M., Wagener, J., Murray-Rust, P., Steinbeck, C., & Wikberg, J. E. (2007). Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinformatics, 8(1). https://doi.org/10.1186/1471-2105-8-59 CrossRef Scholia
\n
", "summary": "Second in a series of articles summarizing articles that cite one of the main CDK articles for CDK News. The first CDK Literature was already half a year ago, so it was about time.", "date_published": "2007-07-14T00:00:00+00:00", "date_modified": "2025-07-30T00:00:00+00:00", "tags": ["cdk"], "_references": [ { "url": "https://doi.org/10.1186/1471-2105-8-59", "doi": "10.1186/1471-2105-8-59" } , { "url": "https://doi.org/10.1021/ac070741j", "doi": "10.1021/ac070741j" } , { "url": "https://doi.org/10.1186/1471-2105-8-105", "doi": "10.1186/1471-2105-8-105" } , { "url": "https://doi.org/10.1002/qsar.200630101", "doi": "10.1002/qsar.200630101" } , { "url": "https://doi.org/10.1021/ci600305h", "doi": "10.1021/ci600305h" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }