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PiSQRD
A web resource that can be used to subdivide protein structures in quasi-rigid dynamical domains. The latter are groups of amino acids behaving as approximately rigid units in the course of protein equilibrium fluctuations. The PiSQRD server takes as input a biomolecular structure and the desired fraction of protein internal fluctuations that must be accounted for by the relative rigid-body motion of the dynamical domains. Next, the lowest energy modes of fluctuation of the protein (optionally provided by the user) are calculated and used to identify the rigid subunits. The resulting optimal subdivision is returned through a web page containing both interactive graphics and detailed data output.
GeoStaS / Geometrically Stable Sustructures
A program with graphical interface which, based on molecular conformations, divides a molecule into "dynamic domains", i.e., parts that stay relatively rigid in all conformations. This division simplifies the description of differences between the conformations. The algorithm implemented in GeoStaS is based on searching for geometrical similarities between atomic motions. The pairwise atomic movement similarity matrix (AMSM) is constructed and then clustered with the use of either specifically adapted nearest-neighbor clustering algorithm (which suggests an optimal solution) or a hierarchical merging algorithm (which requires inputting the number of desired domains). GeoStaS can analyze conformations of both proteins and nucleic acids.
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