{ "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/2008/07/26/cdk-literature-5.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/bsv98-6bz80", "url": "https://chem-bla-ics.linkedchemistry.info/2008/07/26/cdk-literature-5.html", "title": "CDK Literature #5", "content_html": "

Time flies. Another CDK Literature (see also\n#1 ,\n#2 ,\n#3 ,\n#4 ).\nQuite a few papers have been published again, and I’ll briefly discuss a few of them.

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Detection of IUPAC names

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Klinger et al. have written a paper on detection of IUPAC names. As long as semantic markup languages are not the default,\nthis remains important. Remaining problems include correctly finding boundaries in summaries of chemical. The\nCDK has been used to create SMILES.\nRoman Klinger, Corinna Kolárik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M. Friedrich, Detection of IUPAC and\nIUPAC-like chemical names, Bioinformatics 2008 24(13):i268-i276; doi:10.1093/bioinformatics/btn181

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Structure elucidation

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Elyashberg, Williams and Martin wrote a review on structure elucidation and discuss\nSteinbeck’s Seneca software, which uses components of the CDK, though\nthe CDK is not directly mentioned.\nM.E. Elyashberg, A.J. Williams, G.E. Martin, Computer-assisted structure verification and elucidation tools in NMR-based\nstructure elucidation, Progress in Nuclear Magnetic Resonance Spectroscopy, 2008, 53(1-2):1-104,\ndoi:10.1016/j.pnmrs.2007.04.003

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Opensource Distributed Chemical Computing

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Karthikeyan et al. have published ChemStar, an opensource distributed chemical\ncomputing system, build on top the Java Remote Method Invocation architecture, used by the original Seneca too. The\nCDK paper and a Fechner/Guha’s CDK News paper are\ncited in relation to a ChemStar application of benchmarking QSAR descriptors. The article does not seem to mention\nthe opensource license, nor have I yet found a source package download.\nM. Karthikeyan, S. Krishnan, A.K. Pandey, A. Bender, A. Tropsha, Distributed Chemical Computing Using ChemStar:\nAn Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem,\nJ. Chem. Inf. Model., 48 (4), 691–703, 2008. 10.1021/ci700334f

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Taverna’s APIConsumer

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Taverna has several means of making functionality available to the workflow engine. SOAP and BioMoby are two\nprominent ones. The APIConsumer is another one, and described in this paper. The\nCDK-Taverna project lead by Thomas Kuhn,\nis mentioned as another project that uses this approach.\nPeter Li, Tom Oinn, Stian Soiland, Douglas B. Kell, Automated manipulation of systems biology models using\nlibSBML within Taverna workflows, Bioinformatics 2008 24(2):287-289, doi:10.1093/bioinformatics/btm578

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Docking for Substrate Identification

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Favia uses docking to recognize interesting substrates for short-chain dehydrogenases/reductases. The CDK’s\nfingerprinter is used to describe intermolecular similarity, by calculating the Tanimoto distances between the\nbit strings.\nAngelo D. Favia1, Irene Nobeli, Fabian Glaser, Janet M. Thornton, Molecular Docking for Substrate Identification:\nThe Short-Chain Dehydrogenases/Reductases, Journal of Molecular Biology, 2008, 375(3):855-874,\ndoi:10.1016/j.jmb.2007.10.065

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References

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Elyashberg, M. E., Williams, A. J., & Martin, G. E. (2008). Computer-assisted structure verification and elucidation tools in NMR-based structure elucidation. Progress in Nuclear Magnetic Resonance Spectroscopy, 53(1–2), 1–104. https://doi.org/10.1016/j.pnmrs.2007.04.003 CrossRef Scholia
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Favia, A. D., Nobeli, I., Glaser, F., & Thornton, J. M. (2008). Molecular Docking for Substrate Identification: The Short-Chain Dehydrogenases/Reductases. Journal of Molecular Biology, 375(3), 855–874. https://doi.org/10.1016/j.jmb.2007.10.065 CrossRef Scholia
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Karthikeyan, M., Krishnan, S., Pandey, A. K., Bender, A., & Tropsha, A. (2008). Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem. Journal of Chemical Information and Modeling, 48(4), 691–703. https://doi.org/10.1021/ci700334f CrossRef Scholia
\n
Klinger, R., Kolářik, C., Fluck, J., Hofmann-Apitius, M., & Friedrich, C. M. (2008). Detection of IUPAC and IUPAC-like chemical names. Bioinformatics, 24(13), i268–i276. https://doi.org/10.1093/bioinformatics/btn181 CrossRef Scholia
\n
Li, P., Oinn, T., Soiland, S., & Kell, D. B. (2007). Automated manipulation of systems biology models using libSBML within Taverna workflows. Bioinformatics, 24(2), 287–289. https://doi.org/10.1093/bioinformatics/btm578 CrossRef Scholia
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", "summary": "Time flies. Another CDK Literature (see also #1 , #2 , #3 , #4 ). Quite a few papers have been published again, and I’ll briefly discuss a few of them.", "date_published": "2008-07-26T00:00:00+00:00", "date_modified": "2025-08-26T00:00:00+00:00", "tags": ["cdk"], "_references": [ { "url": "https://doi.org/10.1093/bioinformatics/btn181", "doi": "10.1093/bioinformatics/btn181" } , { "url": "https://doi.org/10.1016/j.pnmrs.2007.04.003", "doi": "10.1016/j.pnmrs.2007.04.003" } , { "url": "https://doi.org/10.1021/ci700334f", "doi": "10.1021/ci700334f" } , { "url": "https://doi.org/10.1093/bioinformatics/btm578", "doi": "10.1093/bioinformatics/btm578" } , { "url": "https://doi.org/10.1016/j.jmb.2007.10.065", "doi": "10.1016/j.jmb.2007.10.065" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }