Modeling Structure By Homology

[Douglas Easton]

I am currently modeling the structue of a protein using an X-ray structure for 
a protein, distantly homologous in sequence and in function. I am predicting 
the secondary structure using ssp, nnsp, GOR etc. And alligning  sequence 
homologies and the real and predicted secondary structures. The results seem
neat but my confidence in the approach is a bit shakey.

Does anyone have experience in this?, Know of any particularly good papers?
Can you carry this analysis to the tertiary structure level?

Thanks in advance,
-Doug Easton