I have a pdb file for a protein (3D structure predicted by a tool) and around hundreds of known point mutations in the protein. I want to visualize the protein with all the mutations to see the hub of or core where the mutations are mostly. Is there are tool that does this? I would give the structure in a pdb file and a list of point mutations myself.
Clustering mutations could reveal lots about the protein providing one has the functional impact of each mutation (this cluster are benign, this cluster causes misfolding etc). Many tools are emerging to explore this and there are plenty of established tools that can handle this.
VarMap is a tool that is able to map genomic variant coordinates to the best available structure.