Should I add missing hydrogen atoms in the protein structure predicted by I-TASSER?

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cfas
Posts: 2
Joined: Sat Oct 23, 2021 2:38 pm

Should I add missing hydrogen atoms in the protein structure predicted by I-TASSER?

Post by cfas »

Hello, I have recently started using I-TASSER for predicting some protein structures. However, after downloading the results, I noticed that some hydrogen atoms were not present in the models, but I'm unsure whether these atoms were absent either because 1) the structures were predicted considering a given protonation state or 2) it was a mistake and then I should add the H atoms. If anyone can help, thank you.
jlspzw
Posts: 114
Joined: Tue May 04, 2021 5:04 pm

Re: Should I add missing hydrogen atoms in the protein structure predicted by I-TASSER?

Post by jlspzw »

Hi

Hydrogen atoms is not essential atom for pdb file, even in experimental structure in PDB database, nearly all structure don't contain hydrogen atoms, so you do not need do anything to the predict structure. And most of the program that you use after structure prediction, like function prediction or pymol to check the structure etc not require the hydrogen atoms. based on my knowledge, only MD and ligand docking (perhaps) need hydrogen atoms, but those pipeline actually has the program or method that can allow you do insides those pipeline, so you do not need to warry about it. But if your work need hydrogen atoms, you can check https://zhanggroup.org/C-I-TASSER/C-I-T ... alone/HAAD, it can help you add the hydrogen atoms.

useage ./HAAD input.pdb
then output is input.pdb.h

Best

IT team
cfas
Posts: 2
Joined: Sat Oct 23, 2021 2:38 pm

Re: Should I add missing hydrogen atoms in the protein structure predicted by I-TASSER?

Post by cfas »

Thank you. I'm doing molecular docking and molecular dynamics simulations, I was just uncertain whether I-TASSER added all the relevant H atoms or if I should add the missing ones. For example, when I download a model predicted by I-TASSER and view it in PyMOL or Sybyl, it contains H atoms, but not all of them, so if I click to add missing atoms, the program still adds some of them to the structure. If I understood correctly, in the case of docking and MD simulations, I can add these missing H atoms. Is that correct?
jlspzw
Posts: 114
Joined: Tue May 04, 2021 5:04 pm

Re: Should I add missing hydrogen atoms in the protein structure predicted by I-TASSER?

Post by jlspzw »

Yes, I think docking or MD need H atoms, but those pipeline actually has the program let you add H atoms, what you need to do is following their tutorial I guess, for example Gromacs etc.
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