I known the Pfam database provide the domain information, and we can search a protein's domain information by using the following website, but how to obtain the domain information for a large set of proteins?
http://pfam.xfam.org/search#tabview=tab2
For example, the domain information for protein SOS1 is ( PF00936, PF00169, PF00621, PF00617, PF00618)
Accession ID Description Pdb Interpro
PF00936 BMC BMC domain
PF00169 PH PH domain
PF00621 RhoGEF RhoGEF domain
PF00617 RasGEF RasGEF domain
PF00618 RasGEF_N RasGEF N-terminal motif
You can use batch pfam. (xfam)
http://pfam.xfam.org/search#tabview=tab1
If you need only basic information about domains, such as names, sequences, first and last residue positions, you could use uniprot.org. Uniprot can be easily interfaced with any kind of scripts.
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