Re: [modeller_usage] Using template's ligand as model's ligand

["Ricardo Nicoluci" <>]

Hi,

If I understood what you said, you cant assume the ligand conformation
of your template as the conformation that this ligand will have in the
active site of your model. Some residues might change in your modelled
structure, so you ligand will have a different conformation.

I advise you to use a program to dock this ligand into the modelled active site. 
There is some like: Gold, FlexX  and some that are free to use: DOCK, AutoDock.

Ricardo.

On 6/9/06, Frederico Arnoldi <">> wrote:

Dear Modeller's users,

Could I superimpose the template and the best model of this template and use
the template's ligand as model's ligand? Which are the theorical problem of
doing it if I used Modeller to build the model? How precise is it?

Thanks for the help.

Fred
UNESP - Brazil


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-- 
Ricardo de Paula Nicoluci
PhD Student
Medicinal Chemistry Laboratory
IFSC - University of Sao Paulo
Sao Carlos - SP - Brazil