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On Sun, Oct 18, 2009 at 10:00 AM, Shaun Lott <[log in to unmask]> 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? By default, it looks only at fairly similar hits. It grabs more hits as you pull the similarity threshold down. And if you set that similarity threshold zero, nearly every query gathers half of PDB as potential targets - because small features are shared between many structures. I would be very curious to see an example where SSM *is not able* to catch something that DALI catches - leaving aside SSM limitations like presence of secondary structure and having at least 2-3 SSEs in the common motif. Eugene > 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 >