I have extracted a ligand from PDB native protein and then used that to dock with my hypothetical protein. The hypothetical protein is phosphopantatheinyl transferase and in PDB the crystalized protein was the same but from another organism.
Now if I perform docking to my hypothetical protein with native ligand (from PDB) and check the complex in PROCHECK Ramachandran plot, will it validate my docking study?? I performed blind docking in AutoDock Vina.
I redocked pdb protein with its native ligand and docked my hypothetical protein with the ligand that I obtained from the PDB protein, but in 2D plot the residues are completely different ? How to validate it?
Please help. Thanks---sunzid
All the Ramachandran plot will tell you is the plausibility of the dihedral angles in the protein model. I don't see how this informs a docking study at all.
Procheck is also somewhat dated, Crystallographers have used molprobity instead for decades now.
Agree with Matthew James Conroy. For validation, you have to calculate RMSD between ligand docked pose and crystal ligand, the RMSD value should be within 3 angstroms.
AutodockVina sometimes gives you the conformation of docked ligand outside of the pocket, which you have defined via Grid Box, therefore before submitting to PDBsum you need to confirm the site of docked ligand, it should be present in the defined binding pocket of your receptor.
Okay, thanks everyone for your kind help. I would calculate the RMSD, but the problem is if I count RMSD should I set the cycle number 0, if I set 0 in PyMol it shows me 10.23... and if I don't define cycle , it shows me 2.3 but the residues are cut to 654 from 1050 (Total residues)
Kiran Bharat Lokhande Sir
- Badges
- Science topic
- Similar topics
- Correction