Dear RGs, I want to perform docking studies of Gyrase protein (for example: pdb id : 2XCT) which is in complex with ciprofloxacin which is a standard. the protein has manganese as cofactor (can see in the PdbSum link: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2xct&template=ligands.html&l=1.1) . Here the ligand ciprofloxacin has covalent bonds with manganese cofactor which plays a crucial role in the protein (http://www.ncbi.nlm.nih.gov/pubmed/12051843).
I have removed ciprofloxacin from the complex and performed docking again with ciprofloxacin (externally) using AutoDock Vina. The Vina software won't read metal ions hence leading to inappropriate results as in the attached image file. It is forming 1 covalent bond with Ala419 carbon and Oxygen of ciprofloxacin.
Kindly provide me some ideas to overcome this problem. suggest some servers or tools where docking can be performed including metal ions.
Dear Faun,
Thank you for the reply.
I knew that this can be done in GLIDE which is a commercial tool. But I am devoid of this tool as University cant afford this tool. Plz suggest me with some freely accessible tools.
Yeah Sajin. I am well acquainted with AutoDock4.2 window in combination with MGL tools, and have tried with it.. But I don't know how much accurately I am performing the docking steps in case of metal ions. As I have read through the blogs, it is said that one has to add the specific charge for the metal ion, and in actual I don't know where and how to add. Can you elaborate your ideas in this regard. if possible send me some links and steps...
Our University provides docking facilities in GLIDE software for Research Scholars both in or outside campus.
try Autodock surely it will work and must add parameter file (metal ion) in your docking protocol ( available on their site)
I have came across many posts that asks about docking the ions. I usually follow an alternate strategy as follows if there are co factors in play: You need to have good command over SPDBV in this case...
1. Remove the coordinate bonds between Mn ion and two oxygens from your Ciprofloxacin ligand. You can easily do this from SPDBV. This is a freeware and easy to use.
2. after removal of coordinate bonds save the Ciprofloxacin ligand and Mn ions in separate two pdb files. One for Mn ions and another for ligand. YOu can use this separated ligand for validation purpose as well.
3. Now perform docking. I prefer using Autodock in PyRx environment (again free). after docking locate the dlg file for the run. YOu can load docking results any later time in pyrx if you have closed autodock.
4. After loading dlg file in PyRx, there is option for saving the poses in sdf format. Now save your best pose in sdf format.
5. Convert the best pose (now in sdf format) to pdb format. YOu can use openbabel Gui (again free)
6. after conversion of your docking pose to pdb format, now load your protein and ligand (predicted pose) and metal ions in SPDBV as separate layers and merge these layer in single one.
7 There you have your ligand, metal ions and protein molecule in single file!!
8. You can view interactions between ligand and protein and metal ions in LigPlot + (free for academic users)
hope his help.... AutoDock Rocks...
Adding to the above, please refer to this thread:
https://www.researchgate.net/post/How_can_we_change_the_partial_charge_of_a_pdbqt_file_in_autodock
I am new in this field , using flexX (leadit-2.1.8) for metal ion and protein docking. There is error INVALID MOLECULE when i import metal.mol2/sdf file of metal ion as a ligand .While when any protein .mol2 file import than no problem. Kindly provide me some ideas to overcome this problem.
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