I would like to understand using bioinformatic tools if a peptide interacts with a protein, how can I do it?
you can use a protein as macro molecule and the peptide as ligand , after preparing them in a suitable format you can dock them using autodock vina incorporated in PyRx package/software
In previous literature, it was observed that protein and peptide contain different percent of regular secondary structures. And the existing methods for secondary structure prediction doesn't perform well on peptide structure prediction.
You can obtain the pdp chains of peptides from ccPDB server and develop a model
You can try SWISS-MODEL (https://swissmodel.expasy.org) or PyMol (http://www.pymol.org/) for preliminary predictions, but if you want to know the exact interaction sites, then structural biology technologies, including X-ray crystallography, NMR, and cryo-electron microscopy technology must be used to solve this problem. Recommend an article for you, maybe can help you choose experimental method to determine the structure, https://www.creative-biostructure.com/comparison-of-crystallography-nmr-and-em_6.htm
Hope it helps!
The crucial step is to get the proper structures both protein (target) and peptide (ligand). I guess you have to spend 70% of time to be sure in it. You have to evaluate it using Ramachandran plots\ProCheck\Molprobity\Whatif\Protein health etc. And you have to understand their conformational clusters\landscapes from MD simulations.
We use for this PRIME from Schroedinger.
Then you can try peptide docking procedure of Schroedinger or Rosetta peptide docking. Anyway you have to consider your peptide as flexible molecule and maybe use induced fit option for target as well.
And of course the final MD launch is very desirable.
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