Subject: Summary: Automatic docking with Macromodel

From: Bruno Bienfait <[email-masked]>
Date: Tue, 05 Oct 1999 20:09:13 -0400

Dear CCL,

One week ago I posted :
"
I am interested in automatic docking of small molecules to a protein
using a program equipped with a non explicit solvent model.
I plan to use the MMFF with the GB/SA water solvation model as
implemented in  Macromodel 6.5 for this task. I also would like selected

residues of the binding site to be flexible whereas the rest of the
receptor would be fixed.

According to the user's manual pages 75 and  77, the MOLS option of the
MC, SD and MD related commands can be used for docking searches.
Unfortunately, I haven't found examples or  pratical recipes to perform
automatic docking this way.

Could someone provide  me pointers (references, recipes,  examples)?
"
Thanks to  Marc Zimmer who wrote:

      We have used the MOLS command within a MC search to dock luciferin

into luciferase.        "Site-Directed Mutagenesis of Histidine 245 in
Firefly Luciferase: A proposed Model for the Active Site" B. Branchini,
R.
Magyar, M. Murtiashaw, S. Anderson*, M. Zimmer,  Biochemistry  1998,37,
15311.

--
[ Bruno Bienfait, Ph. D.            Laboratory of Medicinal Chemistry ]
[                                   National Cancer Institute         ]
[ Email : [email-masked]      National Institutes of Health     ]
[ Phone : (301) 402-3111            Building 37, Room 5B20            ]
[ Fax   : (301) 496-5839            Bethesda Maryland 20892 , USA     ]
[ WWW   : http://www.brunob.org                                       ]