Re: Using FEP as non-disruptive mutation procedure

From: Michael Grabe (
Date: Mon Jun 27 2005 - 11:19:13 CDT


if you only select a spherical segment of the protein around the
mutation site when using MODELLER, you will avoid this problem
of having distant parts of the protein being different from your
template structure. there are sample input files in the modeller
tutorial files on how to do this.


On Jun 26, 2005, at 3:10 PM, Leonardo Sepulveda Durán wrote:

> Hello!!!
> I wanted to test the influence of some mutations on a protein. To
> create a mutant I used MODELLER. Nevertheless, modeller always change
> all the protein (althrough only a little) even in places far from the
> mutation site. That would be ok in most of the cases, neverless, I
> have seen differences in the dynamic behaviour far form the mutation
> site, and regarding what i said before i am not sure if it is an
> structural divergence due to the small differeces in nitial structure
> or must be an effect of mutation. I read FEP would be used to do free
> energy calculation of mutation, and I was wondering if FEP can then be
> used as a method mutate which only modifies nearby atoms, and not all
> the structure.
> Thanks
> Leonardo
Michael Grabe, Ph.D.
Post-doctoral Fellow
Howard Hughes Medical Institute
University of California, San Francisco
1550 4th Street GD482
San Francisco, CA 94143
tel: ++ 415.476.4021

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