Creating PDB file for peptide bonds

Question

[tayab soomro]

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.

[Hussain Ather]

It looks like they're available here.

[tayab soomro]

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)

Answer 1

[Joe]

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.

[tayab soomro]

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.

[Joe]

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

[tayab soomro]

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!