The plethora of conformations obtained from biomolecular simulations make it difficult to analyze conformational changes. Geometrically Stable Sustructures (GeoStaS) is 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 is implemented in Java with a user-friendly graphical interface. It is fast (although it depends on the size of the trajectories the user uploads) and robust - it can analyze conformations of both proteins and nucleic acids. There are two types of outputs: (a) a molecule divided into dynamic domains, with coordinates in the PDB format and (b) AMSM matrix, in text format.
The article describing details of the algorithm was published in Journal of Chemical Theory and Computation (J. Romanowska, K. Nowiński, J. Trylska, J. Chem. Theory Comput., 8:2588-2599, 2012, DOI: 10.1021/ct300206j). Please, cite this article if using GeoStaS.
Downloads and source code available at GeoStaS page in BitBucket
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