I have modeled 7 peptides and performed docking in a the catalytic domain of the protein. Our prime object of this study is to identify the catalytic domain residues via known peptide inhibitors. Hence we docked these peptide in this catalytic domain and trying to refined their docking interaction through dynamics simulations. Will this way provide me the refined and validated interactions? Or is there any other way by which I can validate the interaction except wet lab? Please provide your expert suggestion?
Dear saurabh,
Actually experimental measurement is the most reliable method to validate your simulation result but in absence of this method you can compare your your results for various inhibitors. I suggest following analysis for your complexes:
1- Alanine scanning
2- H- bond analysis
3- binding free energy calculation
comparing these analysis for various inhibitors can validate your work.
Hope it helps,
HHA
You can find if the 7 peptides are showing specific binding as follows:
1. Use scrambled peptides for dock (So, you rearange order of one or more of the 7 amino acids in each peptide and see if results change).
2. Check known inhibitors of your protein. Do they bind well at catalytic site? What binding energy do known inhibitors have? Compare values with your peptides.
3. is your protein related to other proteins with similar catalytic pocket? You can try docking your peptides with some closely related protein.
Hope this helps!
Sir, I have docked all seven peptides found that similar binding pattern of catalytic site. will I generate scrambled peptides for all these seven and docked again to catalytic domain ? what will be the benefit by doing this exercise ?
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