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 Post subject: Covalent Docking
PostPosted: Wed Sep 09, 2015 10:54 am 
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Joined: Wed Sep 09, 2015 10:45 am
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Hello all,
I am familiar with non covalent docking in ADT and want to do covalent docking. More precisely using flexible chain procedure
as described in "Covalent docking using autodock: Two-point attractor and flexible side chain methods »
Giulia Bianco1, Stefano Forli2, David S. Goodsell2 andArthur J. Olson2,*
or
"AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility »
Garrett M. Morris1, Ruth Huey1, William Lindstrom1, Michel F. Sanner1, Richard K. Belew2, David S. Goodsell1, and Arthur J.Olson1,3

I understand the principles of flexible SC in these papers but was not able to apply it within ADT.

For now, I have prepared my ligand with modified atoms for bonding to the receptor but really I don’t know where to start
after that. I think I should use first the Setup covalent Ligand in the Flexible Residues menu first but I don’t
really understand the fields in this window (FlexRes and Ligand). Then I guess the next step would be to Choose FlexRes in
the Grid Menu but then…
So I am pretty much lost in this implementation of flexible side chain covalent docking.
Does anyone have some guidance on that with a clear procedure ?

Thanks to all

P. Ladam
Teacher-Researcher
Universite Paris 13


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