Tuesday, October 25, 2011

"Post-doc with experience in CDK programming wanted"

SMARTCyp (see papers below) is an integrated computational approach that mixes cheminformatics with molecular modeling approaches to predict the metabolic fate of molecules. This fate is important to various biological aspects of small molecules, and the metabolism can active a prodrug into a drug, make a toxic compound non-toxic, and a non-toxic compound risky.

The tool has been well received by the community, complementing other approaches. Now, the reason why I blog about these papers now, is that the tool uses the CDK for the cheminformatics parts, which I find really cool. In fact, the project has resulted in good feedback on the CDK. In fact, the project received further funding creating a short-term open position to continue research on enzymatic reactivity of molecules in the cytochrome P450 family, as outlined below.

So, this peer-review is a bit more on the impact of the CDK and SMARTCyp on the academic landscape, than on the content.of the paper.

Patrik Rydberg wrote on the CDK LinkedIn group and the CDK user mailing list about an open post-doc position where CDK expertise is welcomed:
    I'm seeking candidates for a post-doc position in applied cheminformatics at the University of Copenhagen. We are working on drug metabolism prediction models, and our results are as far as possible made into open source software based on the CDK. The group has previously developed the SMARTCyp site-of-metabolism prediction software which is based on CDK, and this project aims to extend the scope of our cytochrome P450 project.

    Employer: department of medicinal chemistry, faculty of pharmaceutical sciences, University of Copenhagen
    Location: Copenhagen, Denmark
    Position: post-doc
    Duration: 7 months, starting january 2012
    Project: drug metabolism by cytochromes P450

    Experiences required:
    Machine learning methods
    java programming

    Bonus for experience in java programming using the Chemistry Development Kit (CDK), experience in development of ligand based virtual screening methods, and experience of work on the cytochrome P450 enzyme family.
The SMARTCyp paper can be found linked to below, with the details of how the CDK and SMARTCyp interoperate and make P450 predictions.

ResearchBlogging.orgRydberg, P., Gloriam, D., & Olsen, L. (2010). The SMARTCyp cytochrome P450 metabolism prediction server Bioinformatics, 26 (23), 2988-2989 DOI: 10.1093/bioinformatics/btq584

ResearchBlogging.orgRydberg, P., Gloriam, D., Zaretzki, J., Breneman, C., & Olsen, L. (2010). SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism ACS Medicinal Chemistry Letters, 1 (3), 96-100 DOI: 10.1021/ml100016x


  1. I might be shooting in my own feet, but I will say it anyway. I think a 7 month contract for a postdoc is a bit like a joke, in terms on length. Wouldn't it be better to hire a freelance for this task and allow him to work from home?

  2. You could ask Patrik if there are other post-doc positions in the group that could extend that time...

    Then again, it could just fill a gap you happen to have around. It's a good university, and a really interesting project!

  3. Just a friendly heads-up: I’m not sure of the policy of on this, but I suspect you might find might they consider advertising is not what their service is aimed at. is (more usually) for science writing reporting on research findings.

  4. Dear Grant, in retrospect, this post may indeed fall outside their window for peer-review.

    Effectively, I think my posts reviews to scholarly impact of the SMARTCyp papers in relation to the CDK work, as such putting the two projects in perspective. I think an open position is a good example that these papers are relevant.

    However, that may indeed not be the kind of the peer-review they are looking for, in which I would absolutely apologize, and remove the researchblogging icon from this post.

    If I am asked too, I will leave a comment here.