Proteins, especially those involved in signaling pathways are composed of functional modules connected by linker domains with varying degrees of flexibility. To understand the structure–function relationships in these macromolecules, it is 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.


We introduce a new tool, mol2sphere, that transforms the atomistic structure of a macromolecule into a series of linked spheres corresponding to domains. It does this with a k-means clustering algorithm. It may be used for visualization or for coarse grain modeling and simulation.

Availability and implementation

PyMOL plugin, source, and documentation SpringSaLaD executables and documentation:, SpringSaLaD v.2 source:

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