[Dock-fans] FW: docking problem

John Irwin jji at cgl.ucsf.edu
Thu Apr 28 22:48:16 PDT 2005

[JJI] I'm forwarding this mail from Shuang Luo. I haven't seen this before,
but perhaps one of you can offer some advice?  

From: shuang luo [mailto:shuang260 at yahoo.com] 
Sent: Tuesday, April 26, 2005 5:22 PM
To: John Irwin
Subject: docking problem

Dear Dr.Irwin:
I found one issue that really confused me. When I docked a ligand which is
cocrystalized with the receptor back to the receptor, the dock pose given by
dock5.2 is similar to the orientation found in the crystal structure (with
RMSD < 1.0). But when I concatnated this ligand with a small library, say 10
ligands, and docked to the same receptor again, the dock gave me a much
worse pose for that ligand (a much poorer RMSD). I plan to use it as a
positive control to tune my docking condition for docking zinc library.
This happened to quite a few protein complex, like ricin, and dihydrofolate
reductase which have crystal structures with different kinds of ligands. I
am not sure if it is the way I use dock causing this problem or this is a
bug. Thank you very much for the help. And looking forward to hearing from
Best regards

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