PFAMPDB {PFAM.db} | R Documentation |
This is an R object that always contains mappings from a PFAM accession (AC) to a PDB ID
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)
http://www.sanger.ac.uk/Software/Pfam/ and ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/userman.txt
#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]] }