thanx so much..
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...
3 answers
Try
PHYRE Protein Homology/analogY Recognition Engine Protein Fold Recognition Server
DescFold(Descriptor-based Fold Recognition System)
Consensus Fold Recognition Methods [PPT]
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains
Also I remember a old Perl program called "Divide-and-BLAST"
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!
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