I am trying to assign fold to a particular domain of a protein. Using the FATCAT server, I found that the fold is similar to the OB fold family ( more precisely SSB proteins).
I read many journals on this OB fold and found that there is little or no sequence homology among the members of this family. I confirmed this by performing structure-based sequence alignment between my domain and members of the SSB family.
Any ideas regarding what else could be done to will be really helpful...
As suggested in the first answer, it is always good to throw a range of fold prediction methods at your sequence. Some may perform better than others and some confidence is gained if several methods give comparable results.
However, for an uncharacterised protein, often prediction can only take you so far. As you mentioned, the OB fold is common to many proteins: here's the SCOP fold entry and the SSB family entry. Fold/domain information can be useful but sometimes, you just can't go any further with computational analysis and it's time for the experimentalists to up their game and generate more data!
Phyre has a great web interface with many options to visualize data.
If you want to try some other methods for protein fold prediction, visit the web site of the CASP competition. You will find many useful tools (perhaps too much).
thanx so much..