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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.

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    $\begingroup$ Mutations can have different effects and severity. "Visualising" them is very powerful for discussion purposes, but quantifying them may be better, see this past Q. You can open your protein in PyMOL and select the residues in the command line part (select interested, resi 1+2+3+5) and then show them (show sticks, interested)... but the problem then the format you have the mutations in influences how you make the concatenated indices... $\endgroup$
    – Matteo Ferla
    Sep 14, 2021 at 9:35
  • $\begingroup$ Also this would be showing the wild type residue, but showing all mutations in a single structure makes no sense in most cases. $\endgroup$
    – Matteo Ferla
    Sep 14, 2021 at 9:36
  • $\begingroup$ @MatteoFerla 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). Indeed a region of no mutations could indicate constraint. $\endgroup$
    – James
    Sep 14, 2021 at 14:48

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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.

PyMol can open PDB files and you can programmatically or manually mutate each position using the mutagenesis tool.

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