[Bioperl-l] fetch protein-na-complexes from pdb

Bernd Web bernd.web at gmail.com
Tue Feb 12 07:45:51 EST 2008


Hi Ulf,

At rcsb.org you can get a list of PDB IDs for Protein/NA complexes and
even download the entries there. See
http://www.rcsb.org/pdb/statistics/holdings.do
Also see "webdownload" on the RCSB site.

Alternatively, you could fetch the files one by one (e.g. with wget).
The file "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt"
contains the entry type of all PDB entries (i.e.: prot/nuc/prot-nuc
and diffraction/NMR).

Regards,
Bernd


2008/2/12 Ulf Lenski <lenski at mdc-berlin.de>:
> is there a bioperl modul for fetching protein-na-complexes from the pdb?
> and can i distinguish ss-dna from dna chains without parsing the pdb
> files and go through the coordinates (calculate distances etc...)?
>
> tx - ulf.
>
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