unique PDB structure files?

Rob Hooft hooft at EMBL-Heidelberg.DE
Thu Jan 4 05:12:37 EST 1996


>>>>> "CL" == Christine Lukacs <lukacs at a.chem.upenn.edu> writes:

 CL> Could anyone out there in crystallography land could direct me to
 CL> a subset of the PDB containing only unique structures?  I want to
 CL> do a search of the PDB, but I don't need to look at, for example,
 CL> chymotrypsin with 10 different small inhibitors.  This would cut
 CL> down on my CPU time immensely...

There are many different possibilities. I can point you to three that
were developed in our group at EMBL:

1) A sequence-unique subset of the PDB, called PDBselect. You can
   choose for youself how sequence-unique you want it to be (down to
   the 25% level)

2) A structure-unique subset of the PDB, part of the FSSP effort.
   This is even smaller than the sequence-unique subset, because
   some unrelated sequences have the same fold. Again different levels
   of similarity can be chosen.

3) The WHAT IF program comes with a relational database that contains
   a sequence unique subset of the PDB, with further restrictions: all
   of them are high quality X-ray structures.

All three can be found on the World Wide Web from our group home page:

   http://www.sander.embl-heidelberg.de/

Since updates of these databases are performed semi-automatically, they
should always be reasonably up-to-date.

Regards,

Rob Hooft
-- 
=== Rob.Hooft at EMBL-Heidelberg.DE   http://www.Sander.EMBL-Heidelberg.DE/rob/ ==
==== In need of protein modeling?  http://www.Sander.EMBL-Heidelberg.DE/whatif/
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