Subject: Automatic docking with Macromodel

From: Bruno Bienfait <[email-masked]>
Date: Mon, 27 Sep 1999 12:57:12 -0400

Hello all

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)?

I 'll summarize the answers.

Thank you

Bruno Bienfait

--
[ 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                                       ]