unique PDB structure files?

Gerard Kleijwegt gerard at rigel.bmc.uu.se
Thu Jan 4 05:39:31 EST 1996


In article <4cf3d8$2hn at netnews.upenn.edu>, lukacs at a.chem.upenn.edu (Christine Lukacs) writes:
|> 
|> Howdy!  Easy question:
|> 
|> Could anyone out there in crystallography land could direct me to a
|> subset of the PDB containing only unique structures?  I want to do a
|> search of the PDB, but I don't need to look at, for example,
|> chymotrypsin with 10 different small inhibitors.  This would cut down
|> on my CPU time immensely...
|> 
|> Thanks!
|> 
|> Christine Lukacs
|> lukacs at anchor.chem.upenn.edu
|> 

use the Hobohm & Sander lists - from the file:



*********************************************************************
*                                                                   *
*                        PDB_SELECT                                 *
*    REPRESENTATIVE LIST OF PROTEIN DATA BANK CHAIN IDENTIFIERS     *
*                                                                   *
*                  UWE HOBOHM & CHRIS SANDER                        *
*                           EMBL                                    *
*                      D-69012 HEIDELBERG                           *
*                                                                   *
*********************************************************************



USE OF THE PDB_SELECT LISTS
*******************************************************************************************************
The representative lists of protein chains are intended for anyone interested in working with currently 
known protein structures. They are intended to save time and effort by offering a representative 
selection that is currently about a factor of five or six smaller than the entire database. Typical 
uses are introductory browsing, analysis of protein architecture, development of prediction methods, 
and model building by modular construction. To use the lists, you need access to data sets from the 
Protein Data Bank and to software that reads protein structure files (see below). 




REDISTRIBUTION AND COPYRIGHT
*******************************************************************************************************
This file may be redistributed freely to anyone provided it is not altered in content or abridged. The
lists may not be sold as such or as part of a service without a license agreement with the authors. 
Copyright by Chris Sander and Uwe Hobohm, August 1992 and later.
In work making use of the list, please cite one of the following:

        U.Hobohm, M.Scharf, R.Schneider, C.Sander: "Selection of a representative set of structures 
        from the Brookhaven Protein Data Bank",  Protein Science 1 (1992),409-417.

        U.Hobohm & C.Sander: "Enlarged representative set of protein structures", Protein Science
        3 (1994) 522



WHERE TO OBTAIN THE LATEST LIST
*******************************************************************************************************
Retrieve the most recent list from the EMBL fileserver by 

- anonymous ftp from ftp.embl-heidelberg.de (192.54.41.33)
     cd to /pub/databases/pdb_select

- www-URL:
     ftp://ftp.embl-heidelberg.de/pub/databases/pdb_select

Questions and/or remarks to:
hobohm at embl-heidelberg.de 




--gerard




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