I'm hoping someone may have come across this one before. I've been using NCBIs Conserved Domain Database and have a list of PSSM IDs I'd like to map to some other ID (such as PDB or interpro) to allow me to work with some of the domain-domain interaction databases.
I've taken a look at the NCBI FTP site (ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/), and the closest I've come is the cdd.versions file which allows mapping between a CD accession number, a 'short name' and the PSSM ID, but I haven't yet found a way to map to PDB or interpro ID.
thanks for this and strange no one needed this before apparently. just a short addition, the file is here ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/fasta.tar.gz (just took some time to notice you were referring to the link in your question) and the aligned sequences are I believe the same CODs reported by different studies from different organisms, some no longer exist in NCBI database, and as I am working on newly sequenced organisms, not clear which of those GIs I should select to use in GO, but I'll go for the first ones