Question: Creating PDB file for peptide bonds
0
gravatar for tayab soomro
17 months ago by
University of Saskatchewan, SK, CA
tayab soomro0 wrote:

I am trying to create a 3D visualization of peptide bonds of amino acids and I was wondering if there was an easier way to get the PDB files for peptide bonds of all of the 20 amino acids.

aminoacids peptide-bonds pdb • 935 views
ADD COMMENTlink modified 17 months ago by jrj.healey12k • written 17 months ago by tayab soomro0
1

It looks like they're available here.

ADD REPLYlink written 17 months ago by Hussain Ather910

These are just the amino acids, I am looking for a pdb file containing the peptide bonds of the amino acids.

So like for example, pdb file for Gly-Ala-Tyr (that's a peptide bond between Gycine, Alanine and Tyrosine)

ADD REPLYlink written 17 months ago by tayab soomro0
1
gravatar for jrj.healey
17 months ago by
jrj.healey12k
United Kingdom
jrj.healey12k wrote:

This is a somewhat hacky way to do it, but I’ve used ITASSER to generate structures for polypeptides as short as 10 AAs in the past.

You just write the fasta by hand, and submit it to be ‘simulated’. This is massively overkill for sure, but shouldn’t take long at all with such a short chain.

ADD COMMENTlink written 17 months ago by jrj.healey12k

I tried this, and it's not quite what I am looking for.

Check this out. I want a similar 3D visualization, except that I want it to be of peptide bonds of certain amino acids.

ADD REPLYlink written 17 months ago by tayab soomro0

I'm guessing now, but tools like JMol, Mercury, and ChemDraw might do this?

ADD REPLYlink written 17 months ago by jrj.healey12k

I looked at the link that Hussain initially posted, and the pdb files for the amino acids aren't too complicated, and I can add connections from one amino acid to another in the pdb files. I might just write up a quick python script to generate pdb files for all the permutations of peptide bonds. Thanks for all the help!

ADD REPLYlink written 17 months ago by tayab soomro0
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