{ "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/2008/01/03/cdk-literature-3.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/rkkty-a3w29", "url": "https://chem-bla-ics.linkedchemistry.info/2008/01/03/cdk-literature-3.html", "title": "CDK Literature #3", "content_html": "

Third in a series summarizing literature citing one of the two CDK articles. See also #1 \nand #2 .

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Reviews

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Two reviews have recently appeared which cite the CDK. Ricard Stefani has written a review in Portuguese of the many NMR-based elucidation tools\non computer-aided structure elucidation. The CDK is cited as a general chemoinformatics tool. It also cites\nSENECA which uses CDK’s structure generators.
\nRicardo Stefani, Paulo Nascimento, Fernando Da Costa, Computer-aided structure elucidation of organic compounds: Recent advances,\nQuimica Nova, 2007, 30(5):1347-1356, 2007, doi:10.1590/S0100-40422007000500048

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Dimitris Agrafiotis has written a overview of the current state of chemoinformatics, and the CDK is cited\nas tool to calculate molecular descriptors. (Jörg is co-author, and\nhe blogged about this article too).
\nDimitris Agrafiotis, Deepak Bandyopadhyay, Jörg Wegner, Herman van Vlijmen, Recent advances in chemoinformatics, J. Chem. Inf. Model.,\n2007, 47(4):1279-1293, doi:10.1021/ci700059g

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1H proton coupling prediction

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I wrote up a separate blog item on this the article Janocchio: Jmol and CDK based 1H coupling constant prediction \nwritten by David Evans at Eli Lilly.
\nDavid Evans, Michael Bodkin, Richard Baker, Gary Sharman, Janocchio - a Java applet for viewing 3D structures and calculating NMR\ncouplings and NOEs, Magnetic Resonance in Chemistry, 2007, 45(7):595-600, doi:10.1002/mrc.2016

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QSAR

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Quantitative-structure-activity-relationship (QSAR) modeling projects are finding their way to the CDK too. Dmitry\nKonovalov cites the CDK as a free source (as in gratis) for descriptor calculation and touches the problem of reproducibility\nof descriptor calculations. Unfortunately, it does not discuss initiatives like the descriptor ontology as is\ndiscussed in the second CDK article ,\nor the efforts discussed in the Blue Obelisk paper (doi:10.1021/ci050400b),\nsuch as the Blue Obelisk Data Repository which aim to improve this reproducibility.
\nDmitry Konovalov, Danny Coomans, Eric Deconinck, Yvan Vander Heyden, Benchmarking of QSAR models for blood-brain\nbarrier permeation, J. Chem. Inf. Model., 2007, 47(4):1648-1656, doi:10.1021/ci700100f

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SOAP webservices

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Xiao Dong and the rest of the Indiana team have set up SOAP webservices,\namong many wrapping CDK functionality, such as descriptor alculation, 2D similarity and fingerprint calculations, and\n2D structure depiction. They also set up a service for toxTree, which itself uses\nthe CDK too.
\nXiao Dong, Kevin Gilbert, Rajarshi Guha, Randy Heiland, Jungkee Kim, Marlon Pierce, Geoffrey Fox, David Wild,\nWeb service infrastructure for chemoinformatics, J. Chem. Inf. Model., 2007, 47(4):1303-1307,\ndoi:10.1021/ci6004349

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References

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Agrafiotis, D. K., Bandyopadhyay, D., Wegner, J. K., & van Vlijmen, H. (2007). Recent Advances in Chemoinformatics. Journal of Chemical Information and Modeling, 47(4), 1279–1293. https://doi.org/10.1021/ci700059g CrossRef Scholia
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Dong, X., Gilbert, K. E., Guha, R., Heiland, R., Kim, J., Pierce, M. E., Fox, G. C., & Wild, D. J. (2007). Web Service Infrastructure for Chemoinformatics. Journal of Chemical Information and Modeling, 47(4), 1303–1307. https://doi.org/10.1021/ci6004349 CrossRef Scholia
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Evans, D. A., Bodkin, M. J., Baker, S. R., & Sharman, G. J. (2007). Janocchio—a Java applet for viewing 3D structures and calculating NMR couplings and NOEs. Magnetic Resonance in Chemistry, 45(7), 595–600. https://doi.org/10.1002/mrc.2016 CrossRef Scholia
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Guha, R., Howard, M. T., Hutchison, G. R., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J., & Willighagen, E. L. (2006). The Blue Obelisk—Interoperability in Chemical Informatics. Journal of Chemical Information and Modeling, 46(3), 991–998. https://doi.org/10.1021/ci050400b CrossRef Scholia
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Konovalov, D. A., Coomans, D., Deconinck, E., & Vander Heyden, Y. (2007). Benchmarking of QSAR Models for Blood-Brain Barrier Permeation. Journal of Chemical Information and Modeling, 47(4), 1648–1656. https://doi.org/10.1021/ci700100f CrossRef Scholia
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Stefani, R., Nascimento, P. G. B. D., & Costa, F. B. D. (2007). Elucidação estrutural de substâncias orgânicas com auxílio de computador: evoluções recentes. Química Nova, 30(5), 1347–1356. https://doi.org/10.1590/s0100-40422007000500048 CrossRef Scholia
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", "summary": "Third in a series summarizing literature citing one of the two CDK articles. See also #1 and #2 .", "date_published": "2008-01-03T00:00:00+00:00", "date_modified": "2025-07-30T00:00:00+00:00", "tags": ["cdk"], "_references": [ { "url": "https://doi.org/10.1590/S0100-40422007000500048", "doi": "10.1590/S0100-40422007000500048" } , { "url": "https://doi.org/10.1021/ci700059g", "doi": "10.1021/ci700059g" } , { "url": "https://doi.org/10.1002/mrc.2016", "doi": "10.1002/mrc.2016" } , { "url": "https://doi.org/10.1021/CI050400B", "doi": "10.1021/CI050400B" } , { "url": "https://doi.org/10.1021/ci700100f", "doi": "10.1021/ci700100f" } , { "url": "https://doi.org/10.1021/ci6004349", "doi": "10.1021/ci6004349" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }