hello.
I want to do protein dimer docking with ligand. is it possible???
because i used protein dimer and ligand and using patchdock, i did protein docking, the result showed only docking of ligand with a protein monomer, so tell how to proceed further.
AutoDock can be used to dock the ligand into the dimer protein. http://autodock.scripps.edu/faqs-help/manual/autodock-4-2-user-guide/AutoDock4.2_UserGuide.pdf
thank you, but is it reliable, i mean the result can be used in papers???
I have a query, we should use protein monomer or dimer for docking?/How to decide on this???
Sajin A K Indu Kumari ... If you can help in this to me.....
For molecular docking, we should look for an article which has described the functional aspect of protein of interest. From review of literature, one should check whether monomer is required for the catalysis of the substrate or dimer of protein is required for the catalysis.
The best answer can be obtained from literature.
Indu Kumari mam, thnku. I looked for the literature too but couldn't find much work done on this protein... can alignment of two subunits be helpful in this???
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