[Genome] protein search using 3D structure information

[Ginger Cheng]

Hello, Browser Gurus,


Please allow me to use this forum to ask a Q for a friend of mine as I 
know there are tons of brilliant minds here, even though it is not so 
tightly pertaining to Genome Browser:

Has anyone tried to find some protein analogs using a 3D structure like 
search, ie, not using the whole amino acid sequence, but maybe some 
discontinuous amino acids, sitting at the most  important motif/3D 
positions of the protein after folding, probably seperated by various 
length of Xs? The 3D structure database only has very limited proteins 
so not very practical at this moment. I'm interested to know if such 
search tools exist myself, as it is one of the most challenging 
algorithms to design and implement but the ultimate goal of analog search


Hope I'm clear. Thanks for any hint

ginger