Mappings from a PFAM Accession number to a PDB ID

Description

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

Details

The PDB ID along with the start point and end point have been attached to the PFAM accessions 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

See Also

• AnnotationDb-class for use of the select() interface.

Examples

## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

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