Convert a molecule into a set of spheres of variable radii for visualization and modeling.
Proteins, especially those involved in signaling pathways are composed of functional modules consisting of long strings of amino acids. These functional “domains” are linked together in geometric arrangements that can be rigid or flexible, depending on the nature of the linker domains. To understand the structure-function relationships in these macromolecules, it would be helpful to visualize the geometric arrangement of domains. Furthermore, accurate spatial representation of domain structure is necessary for coarse-grain models of the multi-molecular interactions that comprise signaling pathways. Here we introduce a new tool, mol2sphere, that transforms the atomistic structure of a macromolecule into a series of linked spheres corresponding to domains. mol2sphere does this with a k-means clustering algorithm. It may be used for visualization or for coarse grain modeling and simulation.
mol2sphere is available as both a plugin for PyMOL on NMRbox and as a new feature within the SpringSaLaD modeling and simulation software (http://vcell.org/springsalad). Source code is available for the PyMOL (and python) implementations on the NMRbox platform at: /usr/software/mol2sphere
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