Virtual Screening for Bioclipse

I recently created a Bioclipse feature to filter chemical structures in a StructureDB database (the new database for chemical structures in Bioclipse). The new plugin is called VScreen, and aims at being a future Virtual Screening feature. Currently the feature is in very early proof-of-concept state with only two simple filters, Molecular Weight and XlogP. Plans include to create an extension point for filters that plugin can extend to contribute new filters.

Currently, the only way of interacting with the plugin is via Bioclipse scripts. A sample usage is available below in a Gist:

A screenshot from Bioclipse is shown below:


  1. Ola, can you say some words on what extension points to use for people who want to write custom filters? E.g. based on that DS algorithm?

  2. Is the slowness (27 s for ~ 800 mols) due to the filter calculation (i.e., XlogP, MW) or is it due to Bioclipse?

  3. Egon: I promise to write up about the extension points in a separate blog. The API is still not fixed...

    Rajarshi: The bad performance is due to non-optimized database interaction. There are many ways to optimize things but we just haven't got there yet :).