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Sunday, June 10, 2007

Janocchio: Jmol and CDK based 1H coupling constant prediction

While looking up a reference for FirstGlance in Jmol, I found Janocchio, a CDK and Jmol based tool for prediction of coupling constants, recently published in Magnetic Resonance in Chemistry. It's written by Evans, Bodkin, Baker and Sharman (from Eli Lilly) and licensed LGPL. It is one of those rare contributions of pharmaceutical industry, and I can only deeply appreciate this contribution.

A quote from the article:
It was therefore decided to create a Java application and applet,
‘JAva NOe and Coupling Calculator with Handy Interactive Operation’ 
(Janocchio), using the open source libraries of the molecular viewer Jmol 
and the Chemical Development Kit (CDK). It aims to provide a simple and
intuitive way to calculate both the NOEs and couplings.


Release 1.0.1 of last May uses an old Jmol, and the CDK release from 26 August 2005. A bit outdated, and I am wondering if it would be a lot of work to integrate this into Bioclipse. Maybe a summer job?
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2 comments:

  1. Anonymous2:22 PM, June 17, 2007

    Hello Egon,

    Thanks for the appreciative post --
    I'm one of the authors of Janocchio.

    With regard to the age of the
    libraries, this was something I was
    going to work on once Jmol 11.2 has stabilised. It currently uses Jmol 11.0.
    Bob Hanson has commented to me that it may be possible to remove the CDK dependency altogether with some changes he has made to the Jmol API.

    Do let me know if there is any interest in integrating this with Bioclipse -- I'm not familiar with that project, but would be happy to look at necessary (hopefully simple :-)) changes to Janocchio with guidance.

    I'd encourage any potential users of
    Janocchio to contact me via the janocchio-users sourceforge list with any questions or feedback.

    Thanks again,

    Dave Evans

    ReplyDelete
  2. Egon Willighagen6:32 AM, June 22, 2007

    Where does the dependency for CDK come in? Jmol in itself does not require the CDK, but can be used as addon...

    ReplyDelete