Time evaluation for calculating molecular descriptors using the cdk

September 7, 2008

To estimate the time needed to calculate molecular descriptors for many molecule (more than 200000) I created a workflow which measured the time needed to calculate each molecular descriptor. This workflow can be found here.

The time needed to calculate different molecular descriptors for 1000 molecules:

Atom typing on natural products with the cdk

September 6, 2008

During some work on natrual products I analysed a proprietary database with over 180000 molecules with the help of cdk-taverna. The aim of the work will be a diversity analysis of natural products. Therefore I have to calculate some molecular descriptors from the cdk. But before I could calculate the descriptors I have to check whether the cdk could handle these molecules or not. Therefore I develope workflow to test how the cdk performs with natural products, especially how many wrong or missing atom types will be detected within this public database.
Therefore I developed the following workflow:

This workflow can be found here on myExperiment.org

For the proprietary database of natural products which contains over 180000 molecules the cdk had only problems with 1350 molecules. Which is less than 0.8 % of the molecules. These molecules has 1854 wrong or failing atom types.

The large number of wrong nitrogens is mainly caused by five bonded nitrogens for which the cdk currently has no atom type defined.

CDK-Taverna at www.myexperiment.org

August 29, 2008

www.myexperiment.org is an open platform which allows users to share their workflows.
Today I started to upload workflows to that platform.
In the next couple of weeks I will upload many more. So if you need examples check out the cdk-taverna group at myexperiment.org

The first workflow I have uploaded loads molecules using an iterative file reader from a MDL SD-file. Each molecule gets stored within a Postgres SQL database which uses the Pgchem::Tigress extension.

Here is an screenshot of the first workflow:

CDK-Taverna mentioned within an publication

August 28, 2008

Egon found a publication some time ago which mentioned the CDK-Taverna plug-in.

see Egon’s post: here

This is the paper:
Peter Li, Tom Oinn, Stian Soiland, Douglas B. Kell, Automated manipulation of systems biology models using libSBML within Taverna workflows, Bioinformatics 2008 24(2):287-289, doi: 10.1093/bioinformatics/btm578