Informative 3D Visualization of Multiple Protein Structures

Lai, P., Church, W.B., Kaplan, W. and Wong, R.K.

With the continued growth of three dimensional structural information databases comes a corresponding increase in interest in this data for the study of new sequences and an ever-increasing incentive to improve automatic structure annotation methods. We examined various methods of presenting structural information in 3D, focussing on means of identifying regions of interest and the display of related structures. Using such information we investigated how this can be used to view variations between structures. As the first choice in bioinformatics searches is often BLAST, we created PyView to examine how best to display its results in 3D, choosing to use the open source Biopython library and the PyMol molecular modelling system as the foundation. Depending on the level of detail involved and number of structures to be shown, different visualisation modes are selected for each structure to be overlaid. Alternatively the domains can be located and highlighted resulting in detailed 3D displays of a protein's structure.

Cite as: Lai, P., Church, W.B., Kaplan, W. and Wong, R.K. (2004). Informative 3D Visualization of Multiple Protein Structures. In Proc. Second Asia-Pacific Bioinformatics Conference (APBC2004), Dunedin, New Zealand. CRPIT, 29. Chen, Y.-P. P., Ed. ACS. 201-208.

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