unique PDB structure files?
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:
Since updates of these databases are performed semi-automatically, they
should always be reasonably up-to-date.
=== 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/
Validation of protein structures? http://biotech.EMBL-Heidelberg.DE:8400/ ====
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