[BiO BB] Template selection

[Yvan Strahm]

Hi Subhash,

You can do a PSI blast using nr as DB and see if after a few round you
will fish other sequences wich structure have been determined. Then
using swissPDBViewer or modeller, see if you can built a descent
model.
Does your sequence produce an acceptable model using 1DMO as template?

Yvan 


On Sat, 5 Mar 2005 16:46:58 +0000 (GMT), Subhash Agarwal
<smagarwal at yahoo.com> wrote:
> Hi all
> 
> I have a protein (GI:56468480), for which i need to
> built a homology model. On carrying blast of this
> protein against PDB sequences, it is revealed that it
> is probably an protein with calcium binding domain. It
> ehibits highest similarity to 1DMO. However on viewing
> the CDD results one is enclined to think that it is
> frequinin.
> 
> My question is that is my conclusion right. Should i
> use 1DMO as template for modelling or a frequnin.
> 
> Thanks
> Subhash Agarwal
> 
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