Examples of Bioclipse exercises

The course and the book Introduction to Pharmaceutical Bioinformatics includes many exercises on typical tasks performed in Pharmaceutical Bioinformatics where you learn how to use Bioclipse. Below follows some examples taken from such tutorials, namely on how to download protein structures and chemical structures.

(Note, that that the below examples assume that you have Bioclipse installed in your computer; if not you can download Bioclipse here. Note also, that the shown examples represent very simple tasks. Bioclipse is a full fledged work-bench that can integrate complex workflows and chemobioinformatics tasks from within one simple user friendly graphically oriented tool.)

1. Downloading protein structures

It is very easy to download protein structures into Bioclipse from the Protein Data Bank (PDB). Use the main menu File > New… in Bioclipse and select Download PDB files, as shown below:

new PDB wizard

Clicking Next allows you to input a comma-separated list of PDB IDs, try for example “1ale,1pdz”. Clicking Finish downloads the file to the selected folder in the Navigator, or to the Virtual project if nothing is selected. The protein 1PDZ is visualized using the Jmol Editor in Bioclipse, as shown below:

Res JMOL 2pdz

You can also use the Bioclipse Scripting Language (BSL) to download PDBs. Below are two examples:

ws query code

2. Query PubChem for chemical substances

It is very easy to download chemical structures into Bioclipse from PubChem. Use the main menu File > New… and select Get structure from PubChem. Clicking Next then brings you to a dialog that allows you to input a PubChem query. Try to downloading “propanolol”, by typing in the drug name as shown below:

Enter search in dlg

Pressing finish downloads the chemical structures that matches the query and places them in the Virtual folder in the Navigator of Bioclipse. Double-click any structure to open it in Bioclipse (see below).
BioClipse full propanolol

Like all functionality in Bioclipse, querying PubChem can also be done via the BSL scripting language from within Bioclipse. Try the following commands and explore the results.