And this is what I call just in time publication:
Davis et al. RosettaLigand Docking with Full Ligand and Receptor
Flexibility. J Mol Biol (2008) pp.
available online today.
Jürgen
On 3 Dec 2008, at 01:47, David Briggs wrote:
Hi there
Assuming you have a model of the complex you are interested in
tinkering with, try submitting it to the Rosetta Alanine Scanning
servery thing.
http://robetta.bakerlab.org/alascansubmit.jsp
By default, it mutates each residue in the interface to ala, does some
local minimisation (side chains only, I seem to recall) and then re
calculates the binding energy. You can also give it lists of other
mutants to try.
If your data is sensitive , you can download the rosetta software and
do it yourself - the rosetta software is a little complicated
sometimes though.
HTH,
David.
2008/12/3 junfeng liu <[EMAIL PROTECTED]>:
Hi Hongmin,
That should need some docking softwares or the structures of the
complex.
ta
liu
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]
<mailto:[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] <mailto:[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
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Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
--
============================
David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
AIM ID: dbassophile
============================
-
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
