Effect of amino acid mutation (deletion) on the protein structure

Question

[pixie@bioinfo]

I have a wild-type amino acid sequence of a plant. I have a mutated sequence with a single amino acid deletion. I have modeled the protein structure and computed the H-bonds and performed energy minimization using SPDV (swiss PDB viewer). Now, I need to delete a particular residue and perform the same exercise. How do I go about it ? Any suggestions for softwares/servers ?

[lieven.sterck]

just delete the AA and re-do the analysis you already did? But I'm probably missing something? Do you first need to determine which particular residue you need to delete?

[Joe]

I know there is software out there that can edit PDB files though I don’t know many by name.

I believe UCSF Chimera has structure editing options, alternatively you could manually edit the PDB by hand (or do so using BioPython etc). The latter option (unless you use Biopython) is probably non-trivial, since you’d need to make up some amino acid coordinates.

See: https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ

You’ll need to repeat your process of energy minimisation etc, whatever you do though.