ADL: Method of covalent docking

Rudy J. Richardson rjrich at umich.edu
Mon Sep 20 06:30:39 PDT 2010


Nok,

It is my understanding that autodock cannot do quantum mechanics 
simulations or simulations involving making/breaking of covalent bonds. 
However, you could use autodock to study the formation of a Michaelis-type 
complex of a protein and ligand, before covalent attachment of the ligand 
to the active site. You could then use other programs to do 
energy/geometry minimizations of a protein with a mutated residue that has 
the ligand covalently attached.

Best wishes,

Rudy

On Mon, 20 Sep 2010, Nok :p wrote:

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> Rudy,
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> Thanks you very much for your time to suggest my problem.
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> Now I try to redock of isocitratelyase with its ligand (pdb code = 1f8m). In binding pocket. I found that this ligand bind with its target that I call "covalent docking".
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> I tired to delete this bond in order to separate ligand out. And then I try to do step by step of ADT 4.2. I think my method is wrong. Please suggest me.
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> Thanks in advances
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> Best regards,
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> Nok
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