Dear Gloria, If you are searching with a protein sequence, you could also try FFAS (ffas.burnham.org/). This will perform profile-profile alignments to do fold recognition. Works quite well for low homology cases in particular.
HTH and best wishes, Mohammad
--- Begin Message ---We have a protein sequence that probably contains OB folds. What is the best way to search for the top structural homologs to this sequence in the pdb? G
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