Non-related proteins can have very different structures, but when they share a common biological function, often they share a common 3D substructure that realizes this function: this is a motif. Here, we investigate here a geometric method to detect such similarities between two protein structures.
When several instances of the same motif are known in different proteins, it is useful to merge the geometric and chemical information of each observation in order to obtain a much more accurate model of the motif. We demonstrate here how this could be done with the heme binding motif.