Hi Hari,
Right terminal residues for constructs.
some time back there was some discussion with this subject.
you can check that threads also.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Tue, Mar 31, 2009 at 5:10 AM, Ho-Leung Ng wrote:
Hello Hari,
The general rule is to truncate/delete residues that are
predicted to be disordered, for example, by secondary structure
prediction or homology modeling. You do have to be careful as there
may be functionally important, conserved, structured loops that you
want to retain. However,
Our meta-tool for construct design:
http://xtal.nki.nl/ccd/Welcome.html
More or less similar to what Kornelius showed, but skipping the
alignments
(since most secondary prediction tools do that internally anyway)
plus it lets you choose your starts and ends, and it also designs
primers fo
Hi -
we normally use:
http://toolkit.tuebingen.mpg.de/hhpred
together with:
http://toolkit.tuebingen.mpg.de/quick2_d
Both routines have a nice interface and a very sensitive and novel CS-Blast
algorithm which can be used/integrated into the search.
Best wishes
Kornelius
On Mon, 30 Mar 2009
Hi,
There are several semi-rational ways to design constructs on the basis of
existing structures. It is important to remember that we only partially
understand the protein expression and folding - which means that sometimes
(way more often then I'd like) all the design considerations have to go
o
