link between SCOPE and PFAM

Question

[fyfes]

Hello, is SCOPE and PFAM domain annotation different? Is it possible to get a SCOPE id for a PFAM id?

Answer 1

[Mensur Dlakic]

I am assuming that you are asking about SCOP or SCOPe.

Generally speaking, Pfam and SCOP domain annotations are different. SCOP domain assignments are based on expert examination of folded units within structures, while Pfam domains are derived from sequence alignments. In many cases the two assignments will be similar, but not always.

If you are asking for a single file that shows global correspondence between Pfam and SCOP, I am not sure that such a thing exists. However, there is a file here showing the correspondence between Pfam and PDB structure IDs, from which one could figure out links to SCOP. Also, at each Pfam family page there are indirect links to SCOP if there is a domain structure available. For example, if you go to this methyltransferase family, there is an "Example structure" link on the right-hand side. You can even change a PDB ID if there are multiple structures available, and follow the link to the next page that will display a SCOP link among several others.