Question: Effect of amino acid mutation (deletion) on the protein structure
gravatar for pixie@bioinfo
2.1 years ago by
Université Paris, Saclay
pixie@bioinfo1.4k wrote:

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 ?

structure mutation protein • 1.3k views
ADD COMMENTlink modified 2.1 years ago by RamRS30k • written 2.1 years ago by pixie@bioinfo1.4k

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?

ADD REPLYlink written 2.1 years ago by lieven.sterck8.7k

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.


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

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Joe18k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1132 users visited in the last hour