Project Aims
Structural biology is an essential component of current molecular bioscience teaching. However, it requires students to develop an understanding of 3-dimensional (3D) structures that is difficult to acquire from conventional teaching methods using 2-dimensional images, in either books or lecture slides. This is an example of how a publicly available online database can be queried, and information combined with other data and visualised using a semantic tool.
The Development Process
Linking datastreams from the Protein Data Bank and open access publications
This web application has been built using Exhibit, as an example of a visualisation tool using different sources of data about proteins and integrating an open source 3D visualisation tool (Jmol). The test data set is based upon the ‘Molecule of the Month’ series from the Protein Data Bank (PDB). The application uses data from a JSON file, which was converted from an Excel spreadsheet. The spreadsheet included three types of data for each item: its name, its PDB identifier, and a keyword about the type of protein.
The Exhibit is written in such a way that on the basis of this small amount of information, the application can dynamically pull in thumbnails of proteins from PDB web services, load 3D structural files from the PDB into Jmol within popup windows, and can also query the PubMed online database for papers related to the protein involved.
Link
Public Website: http://www.ensemble.ac.uk/projects/plantsci/pdb/3d_molecules.html
Further Information
- Jordan, K. and Johnstone, K. (2008) ‘Using interactive 3-D models in teaching’ Higher Education Academy Bioscience Spring Bulletin 2008
- Jordan, K. and Johnstone, K. (2009) Exploring 3D Molecular Structures with Exhibit. Poster presented at Ensemble Project seminar, 8th January 2009, St John’s College, Cambridge
