[Dock-fans] anchor and rigid docking using 2 anchor points

Marsia Gustiananda marsia at eijkman.go.id
Wed Jul 21 13:38:09 PDT 2010

I'm a new dock user.

I've been trying to do macromolecular docking. I tried rigid docking and it worked OK (I can regenerate the crystal structure of the complex).  And the reason for that I think is because the ligand has been in a right conformation for docking.  The ligand is a 9 mer peptide, and the protein is MHC. Then, I tried anchor and rigid docking, and this was not successfull. It seems that dock choose one anchor point, which is the ring structure in the middle of the peptide, and then grow from that point.  According to the literature, residue no 2 and residue no 9 of the peptide is the anchor points in the peptide-MHC complex. My question is: Is it possible to set up two anchor points for anchor and rigid docking?  After anchoring, then I need to close the loop between these 2 anchors.
If so, how do I modify the input file? and what other things necessary to be able to do it?

Thank you.


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