<p>Is anyone aware of a tool which allows one to apply the concept of &quot;mutation hotspots&quot; to 3D protein structures? It is common to define mutation hot spots at the DNA level where we define the hotspot as a region of DNA sequence with recurrent mutations. But what if we want to know if some mutations are &quot;geographically&quot; co-located in the 3D protein structure (e.g., in the same pocket) but not necessarily &quot;sequentially&quot; co-located. Even without pre-defined concepts of &quot;pockets&quot; if a protein structure is known then it should be possible to define some concept of physical distance between residues. Any suggestions?</p>

It looks like you can also visualize mutations for certain genes in a 3D context using [CBioPortal][1]. Enter a gene such as ESR1. The select the 'Mutations' tab. Then hit the '3D Structure' button beside the mutation diagram (loliplot) that shows the 1D location of observed mutations along the amino acid sequence. This opens a side panel that shows a 3D model for each PDB chain that is available for your protein of interest. You are also give some ability modify the 3D visualization and the way mutations are annotated on it. Very slick interface.

 [1]: http://www.cbioportal.org/public-portal/