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 domain definition, try http://pdomains.sdsc.edu/ which offers a handy interface for comparing a number of different methods for automatic domain calling. hope this helps Shaun
