PFAMPDB2AC {PFAM.db}R Documentation

Mappings from a PDB ID to a PFAM Accession number

Description

This is an R object that always contains mappings from a PDB ID to a PFAM accession (AC)

Details

The PFAM accession number has been attached to the PDB IDs in this object.

More Details: PDB (http://www.rcsb.org/pdb/index.html), the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. Reference: H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research , 28 pp. 235-242 (2000)

References

http://www.sanger.ac.uk/Software/Pfam/ and ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/userman.txt

Examples


        #To map from PDB to PFAM IDs:
        x <- PFAMPDB2AC
        # Get the PDB identifiers that are mapped to a PFAM ID
        mapped_keys <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_keys])
        if(length(xx) > 0) {
          # Get the PDB ID for the first five CAZYs
          xx[1:5]
          # Get the first one
          xx[[1]]
        }


[Package PFAM.db version 2.2.0 Index]