[gmx-users] Mutagenesis

Esther Caballero-Manrique ecaballe07 at gmail.com
Tue Aug 7 09:16:33 CEST 2007

Hi everyone,

I am new to mutagenesis studies, so I was wondering if I could get some
input on my approach. My task involves mutagenizing a residue (with all  19
possibilities)  in a protein that binds DNA, and then deciding whether the
resulting structure is physically acceptable.
My approach to do this is 1) mutate using MODELLER,
2) check the structure with something like PROCKECK (although since I am
just mutating one residue, this doesn't seem important/useful),
3) align the resulting structure from MODELLER with the original and paste
the DNA
4) check for clashes with PROCHECK, and
5) do MD to see whether the model is feasible/calculate free energy of
Obviously all steps are easy and fast except the last one, and my question
is, does anyone think that step 5 is overdoing it if one just needs to know
whether a structure is feasible (i.e., I am not using MD for refinement, but
as a check of the feasibility of the complex)? Does anyone have a
better/easier way to do this?

Thanks a lot for your help,

Esther Caballero-Manrique
Unit of Cancer Pathology
Center for Excellence in Research on Aging
University "G. D' Annunzio"
Via Colle dell' Ara
66013 Chieti Scalo (Chieti), Italy
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