Structure similarity search

[Richard P Grant]

Hi people,

Given a protein domain structure (100 amino acids) we would like to search
for similar domains in (a) 1 protein (b) the entire sequence databases.
The problem is of course that there is no solved structure for (a) and
most of (b).... so some form of prediction, threading or modelling will
have to be done as part of the search/comparison.

Ideas?  I can't find exactly what I want on the Web, although the most
excellent PredictProtein service in Heidelberg may do what we want.
We're looking for either an internet-based resource, or a standalone that
will run under Unix or MacOS.

Thanks, please followup to bionet.software so that everyone can see if
there is a solution.

--
Richard P. Grant  MA  DPhil          University of Oxford | rgrant at molbiol
http://www.molbiol.ox.ac.uk/~rgrant  FFPGP                | .ox.ac.uk
-----------------------# Trust me - I'm a doctor. #-----------------------