Roberto Sanchez wrote:
As a supplementary question, does anyone know where I could download the PDB (or even the ExPDB) database - sequences only, in a FASTA or BLAST format ?ftp://ftp.rcsb.org/pub/pdb/derived_data/
There is also 'pdbaa': ftp://ftp.ncbi.nih.gov/pub/blast/db/pdbaa.Z and ASTRAL (derived from SCOP which in turn is derived from the PDB): http://astral.stanford.edu/There are a number of very complex issues regarding the mappings between FASTA sequence files of the PDB and the actual structural data. The ASTRAL pages and literature address these issues.
Caveat biologist.