On Sun, Oct 18, 2009 at 10:00 AM, Shaun Lott wrote:
> In my experience, DALI can be better than SSM at detecting distant
> structural similarities.
this is interesting. Do you take into account that, in difference of DALI,
SSM
has a control on the remoteness of structural hits that it delivers?
In my experience, DALI can be better than SSM at detecting distant
structural similarities. You might also want to try CE. To decide if a fold
is 'new' rather than 'old but decorated' often boils down to a somewhat
subjective call, but asking Alexei Murzin is as good a way as any to decide :-)
For
On Friday 16 October 2009 15:49:16 Demet Arac-Ozkan wrote:
> Dear All,
>
> I have a few questions about protein structure and fold. I will appreciate
> your suggestions:
> We have the crystal structure of a protein and it looks like it might be a
> new domain.
>
> 1) Our structure looks like t
SSM is your friend there: http://www.ebi.ac.uk/msd-srv/ssm
HTH,
Fred.
> Message du 17/10/09 00:59
> De : "Demet Arac-Ozkan"
> A : CCP4BB@JISCMAIL.AC.UK
> Copie à :
> Objet : [ccp4bb] domain boundary, new fold, structure-based sequence alignment
>
>
> Dea
Dear All,
I have a few questions about protein structure and fold. I will appreciate your
suggestions:
We have the crystal structure of a protein and it looks like it might be a new
domain.
1) Our structure looks like there are two domains however there are some close
interactions between the
