Max-Planck-Institut für Informatik
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Version 3.1, March 2007

For many proteins, alternative structural models determined by X-ray crystallography or NMR spectroscopy, are frequently available in PDB. These models can present significant structural dissimilarity. STRuster is a method for comparison and analysis of these alternative structural models.

Two main type of analyses are performed: clustering and identification of variable and invariant regions. Hierarchical clustering reflects the hierarchy of similarities between all pairs of models. A dissimilarity value based on the differences between carbon alpha distances is used for clustering. The identification of variable and invariant regions is based on the analysis of the distribution of the standard deviations of the carbon alpha distances, where variable regions have higher (absolute or relative) distance standard deviations. The different invariant regions are visualised by optimal structural superposition.
The method is described in:
The method has been applied to analyse the domains at the species level of SCOP (1.71 release). You can query the results by PDB ID, SCOP species sunid code, or access the list of all available results. For more information see Help/Info.

For questions comments contact:
Francisco S. Domingues
Computational Biology and Applied Algorithmics

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STRuster is part of the BioSapiens Network of Excellence.
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