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On Thu, 22 Aug 2013, Gloria Borgstahl wrote: > 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 Hi Gloria, If you expect decent sequence simnilarity to one or more proteins in the PDB, and if you don't have the structure of your protein, a simple FASTA search should give you the list of hits and alignments quickly. I would do that using the PDBeXplore FASTA archive browser - http://pdbe.org/fasta Simply provide your sequence (or UniProt accession) and submit. If there are hits, they will be presented in a way that allows for rapid further exploration, e.g. in terms of their CATH classifications, bound ligands or Pfam families. You can also sort the hits by E-value or %-age identity (amongst many other things) and get the alignments with your sequence in the results page. If you want to explore the interface, try http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/?seq=SVRKFTEKHEWVTTENGVGTVGISNFAQEALGDVVYCSLPEVGTKLNKQEEFGALESVKAASELYSPLSGEVTEINKALAENPGLVNKSCYEDGWLIKMTFSNPSELDELMSEEAYEKYIKSIEE&tab=PDB%20entries (this uses the sequence of PDB entry 3KLR which also has an OB fold, CATH class 2.40.50). There are a number of PDBeXplore modules available (http://pdbe.org/explore), including a CATH-based browser (if you should like to analyse all the structures that contain an OB fold according to CATH). If you should have a structure, you can use PDBeFold (SSM; http://pdbe.org/fold) to quickly find and compare similar structures without taking sequence into consideration. --Gerard