Using FEP as non-disruptive mutation procedure

From: Leonardo Sepulveda Durán (
Date: Sun Jun 26 2005 - 17:10:17 CDT


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.



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