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
