Eventually you will have to make the mutant for a reviewer. So in
silico will only give you perhaps some ideas but there's no way of
avoiding wetlab.
Jürgen
On 2 Dec 2008, at 22:38, Hongmin Zhang wrote:
Thanks! I think we still can't tell if the mutant would disturb
ligand binding or not.
Best!
Hongmin
On Wed, Dec 3, 2008 at 2:15 PM, Juergen Bosch
<[EMAIL PROTECTED]> wrote:
In that case you might want to use CNS with model_anneal.inp or
model_minimize.inp, or the equivalents in phenix
Jürgen
On 2 Dec 2008, at 21:29, Hongmin Zhang wrote:
Yes, it is better to have MD or energy minimization. Otherwise,
with only view on the screen, we can't tell if the mutated residue
would disturb ligand binding because of the side chain flexibility.
Best!
Hongmin
On Wed, Dec 3, 2008 at 12:50 PM, Juergen Bosch <[EMAIL PROTECTED]
> wrote:
Pymol
the question is, into how much trouble do you want to get ?
MD simulations ? Energy minimisation ? Then you will need to do
more than just mutate on the sreen one residue with Pymol.
Jürgen
On 2 Dec 2008, at 17:29, Hongmin Zhang wrote:
Dear All,
I am trying to mutate a single amino acid in a PDB to see if the
mutant
disturbs ligand binding. Does anyone know any software that can do
such work?
Thanks a lot!
-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
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Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
