Hello, Research Community (RA),
I am looking to use a Pepsite2 bioinformatic tool for computing the binding residues of receptors (ACE) when used with food peptides. Please let me know if the enzyme model is required to prepare for that. I mean to say this tool asks for the PDB code and chain id of an enzyme that can be easily found from the protein data bank. But is there any treatment needed for this PDB structure like removal of a lisinopril inhibitor or water molecules?
Dear Sonu Sharma , you need to prepare the protein file by removing the inhibitors with Pymol software, then you have to prepare the protein file by removing molecule waters, add hydrogens and equilibrate charges, I think this can be done with MGLTools. I advice you to check if your protein had already been docked and if they mention the location of the action site.
best regards.
Hi Hicham, thank you very much. I am taking PDB structure of ACE(1O8A) from the protein data bank. Are you sure about using Pepsite2 software? I know that for molecular docking, it is required to prepare the protein structure but for use in this software, I am doubtful.
Dear Sonu Sharma , i m not 100% sure about the preparation process for pepsite2 for the second uploading option. If you use the first option where you enter the PDB code you don't need any preparation, you can see in the results that they have removed the inhibitors, but no idea If you add the PDB file manually, I advise you to try the second process with a protein that had been already processed with this software, take anyone from the literature. I wish you the best.
kind regards
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