<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>

Some additional options:

 - [Mutation 3D][1]
 - [HotSpot3D][2]
 - [HotMAPS][3]

 [1]: http://www.ncbi.nlm.nih.gov/pubmed/26841357
 [2]: https://github.com/ding-lab/hotspot3d
 [3]: https://github.com/KarchinLab/HotMAPS