Compare similarity of protein variants
I have some .pdb files with structures of variants of the same protein and I'm looking for a way to quantify how similar (or dissimilar) they are from a reference protein.
I've tried superimposing them and calculating RMSD with ChimeraX or PyMol, the problem I'm having is that some variants are shorter than the reference (truncated proteins) and I would like to take this into account, so comparing the common residues is not a good option for me.
What would be the best way to quantify how different the protein structures are?
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You could try another metric like TM-score (as used by the ITASSER server). It does a similar thing to RMSD, but in my experience 'breaks' less easily in the edge cases like you describe.
You could also look at foldseek, it's akin to blast but for 3d structures and uses pdbs as input for both database generation and search queries.
I doubt it would be anywhere near as accurate as TM-score, as suggested, but if you have lots of comparisons it would be a very useful and fast filter to remove obvious mismatches. Though it only gives you a score on similarity likelihood, and not dissimilarity. You could also filter results to only include matches with +n% of query and target sequence to reduce partial hits if required.