Software
VASCo: computation and visualization of annotated protein surface contacts
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* Corresponding author: Georg Steinkellner georg.steinkellner@uni-graz.at
1 Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010 Graz, Austria
2 Research Centre Applied Biocatalysis, Petersgasse 14, 8010 Graz, Austria
3 Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
4 Christian Doppler Laboratory for Genomics and Bioinformatics, Petersgasse 14, 8010 Graz, Austria
BMC Bioinformatics 2009, 10:32 doi:10.1186/1471-2105-10-32
Published: 24 January 2009Abstract
Background
Structural data from crystallographic analyses contain a vast amount of information on protein-protein contacts. Knowledge on protein-protein interactions is essential for understanding many processes in living cells. The methods to investigate these interactions range from genetics to biophysics, crystallography, bioinformatics and computer modeling. Also crystal contact information can be useful to understand biologically relevant protein oligomerisation as they rely in principle on the same physico-chemical interaction forces. Visualization of crystal and biological contact data including different surface properties can help to analyse protein-protein interactions.
Results
VASCo is a program package for the calculation of protein surface properties and the visualization of annotated surfaces. Special emphasis is laid on protein-protein interactions, which are calculated based on surface point distances. The same approach is used to compare surfaces of two aligned molecules. Molecular properties such as electrostatic potential or hydrophobicity are mapped onto these surface points. Molecular surfaces and the corresponding properties are calculated using well established programs integrated into the package, as well as using custom developed programs. The modular package can easily be extended to include new properties for annotation. The output of the program is most conveniently displayed in PyMOL using a custom-made plug-in.
Conclusion
VASCo supplements other available protein contact visualisation tools and provides additional information on biological interactions as well as on crystal contacts. The tool provides a unique feature to compare surfaces of two aligned molecules based on point distances and thereby facilitates the visualization and analysis of surface differences.