Thursday, January 03, 2008

CDK Literature #3

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

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

Dimitris Agrafiotis has written a overview of the current state of chemoinformatics, and the CDK is cited as tool to calculate molecular descriptors. (Jörg is co-author, and he blogged about this article too).
Dimitris Agrafiotis, Deepak Bandyopadhyay, Jörg Wegner, Herman van Vlijmen, Recent advances in chemoinformatics, J. Chem. Inf. Model., 2007, 47(4):1279-1293, doi:10.1021/ci700059g

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

Quantitative-structure-activity-relationship (QSAR) modeling projects are finding their way to the CDK too. Dmitry Konovalov cites the CDK as a free source (as in gratis) for descriptor calculation and touches the problem of reproducibility of descriptor calculations. Unfortunately, it does not discuss initiatives like the descriptor ontology as is discussed in the second CDK article, or the efforts discussed in the Blue Obelisk paper (doi:10.1021/ci050400b), such as the Blue Obelisk Data Repository which aim to improve this reproducibility.
Dmitry Konovalov, Danny Coomans, Eric Deconinck, Yvan Vander Heyden, Benchmarking of QSAR models for blood-brain barrier permeation, J. Chem. Inf. Model., 2007, 47(4):1648-1656, doi:10.1021/ci700100f

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


  1. A few more articles cited the most recent CDK publication

    Ingsriswang S, Pacharawongsakda E
    sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets
    BIOINFORMATICS 23 (18): 2498-2500 SEP 15 2007

    Rosania GR, Crippen G, Woolf P, et al.
    A cheminformatic toolkit for mining biomedical knowledge
    PHARMACEUTICAL RESEARCH 24 (10): 1791-1802 OCT 2007

    Yang ZR, Hamer R
    Bio-basis function neural networks in protein data mining
    CURRENT PHARMACEUTICAL DESIGN 13 (14): 1403-1413 2007

    Micheli A, Sperduti A, Starita A
    An introduction to recursive neural networks and kernel methods for cheminformatics
    CURRENT PHARMACEUTICAL DESIGN 13 (14): 1469-1495 2007

  2. Thanx. Already had them (with two more) lined up for #4.

  3. There is an English version of the CASE system review at Curr_Meth_Med_Chem_Biophys. Pages 101-123, 2007.

    You might want to read it. It is one of the weakest reviews of CASE I have seen in a long time and is factually incorrect in a number of areas. It wrongly associates products from one company with another one...for example PredictIt is not an ACD/Labs product. It is 2 years out of date in terms of reviewing products and didn't do a good job reviewing recent literature at all in my opinion - there is one article in the list of references from later than 2004. That one article from 2006 was written by the authors of the review article itself. Overall I don't think it was well researched.

    I hope the review of the CDK were accurate.

    I understand that I've just opened myself to similar types of negative reviews of my own articles :-)

  4. Hi ChemSpiderMan... this is why I love the blogosphere... I had not read the full article yet, just scanned how the CDK was mentioned, as I normally do for CDK Literature... The CDK Literature series is not about reviewing all that literature, but just giving an overview of what literature cites the CDK.

    I always find it disturbing when peer-reviewed literature is so wrong. This clearly indicates that the peer-review system is not working. And this does not only apply to less-well-known journals, but for more high-profile journals too...

    And which scientist picks up the pen and write a letter to the journal...

    An incorrect paper needs a negative review. The comments don't, however, have to be on the person, but should be factual. If we stop correcting each other, we harm science. I don't mind negative critique on my work, as long as it is constructive and based on scientific arguments.

    BTW, do you got an URL or DOI for the paper? Cannot find it with Google(-Scholar) or Web-of-Science...

  5. Here, Here to your comments. I will post, soon I hope, about my recent experiences of the peer-review process and my growing disappointment with the way that the process is being handled. I've authored/co-authored over a dozen publications during the past year and my experience is one of frustration.

    I could not find a DOI for that article.

    I agree with the objectivity regarding commenting on the science and removing the personalities from the discourse. That's not happening very well in my opinion, even in our own rather tight blogging circles. I've asked objective questions of others on a number of occasions only to receive rather nebulous answers and certainly not addressing the specific questions directly. We're all "people" and switching off the emotions, while difficult when handling the "defence" of our science, can be done.

    YOu might have heard that Christoph S. was a little perturbed by our treatment of his CASE systems in our publications on Structure Elucidator. However, a short face to face in Chicago, and a commitment to work through it, led us to share information quickly and we went on to author a publication together soon after. Similarly, Wolfgang Robien and I have differed in opinions regarding NMR prediction on a number of occasions but I have much respect for him as a scientist, have enjoyed every time I have met with him and he and I also have shared opinions about NMR and science (you've likely seen that on PMR's blog).

    Our informatics technologies are developing...the "judge" within each of us makes us human but continues to get in the way of objective science on a regular basis.