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STRuster

Thank you very much for your interest in using the Struster service. Unfortunately we had to discontinue the service due to the closing of the Department for Computaional Biology and Applied Algrithms at the Max Planck Institute for Informatics, in the wake of the retirement of its Director Thomas Lengauer. We ask for your understanding.

Description

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.

Method

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: Domingues FS, Rahnenführer J, Lengauer T. Automated clustering of ensembles of alternative models in protein structure databases. Protein Eng Des Sel 2004 17:537-543. Domingues FS, Rahnenführer J, Lengauer T. Conformational analysis of alternative protein structures. Bioinformatics 2007 23:3131-3138.

Results

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.

• Results for PDB ID / SID:  
• Result for SCOP species sunid:  
• View list of results.

Download

• Source code of the STRuster library is available.
• The estimates of coordinate uncertainty based on DPI are available.

For questions comments contact:
Francisco S. Domingues doming@mpi-sb.mpg.de
Computational Biology and Applied Algorithmics

STRuster is part of the BioSapiens Network of Excellence.

• Algorithms & Complexity
• Computer Vision and Machine Learning
• Internet Architecture
• Computer Graphics
• Databases and Information Systems
• Research Group Computational Biology
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    • STRuster
• Automation of Logic