Hi everyone,
I have to dock DNA with a ligand (cordinated with Mn and Cl). I can use autodock for it? If yes, is there any difference in protocol protein docking and DNA docking in autodock?
If autodock can not be used for DNA docking then what other program or server I can use for it?
Thank you in advance
In general yes - autdock has parameters for DNA and the protocol in principle is the same. In your case Mn will cause problems, since most likely there are no parameters for it implemented in autodock. If it makes sense to remove the MnCl part, do that. If not, there are ways to add these parameters, just google for them or see other topics on ResearchGate on it.
Docking of DNA ligand is much similar to protein ligand docking. In your case, you should choose DNA as the macromolecule and the rest are same. Since Mn is not recognized by Autodock, you can add parameters (http://autodock.scripps.edu/faqs-help/faq/faqsection_view?section=Scientific%20Questions).
Save the attached file in your working directory and use it in the parameter step of your autodock.
Hope this works
Dear Vikram Dalal,
Indeed, the methodology will remain unchanged but, you have to have add parameters for Mn.
Dear Vikram,
In addition to the above comments, the modeling and simulation of DNA requires careful consideration of solvent and counterion atmosphere to ensure system stability.
https://www.ncbi.nlm.nih.gov/pubmed/8800475?dopt=Abstract
Thank you all.
I have to ask one more thing. one of my ligand has Mn, Cl and even water. I have to docked it with protein and DNA.
Upto now, I docked normal ligand (without metal or water) with protein (without metal or water).
So, What other things I have to consider for DNA and protein docking with ligand (Mn, Cl and water)?
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