quick title search of PDB

Reinhard Doelz doelz at comp.bioz.unibas.ch
Tue Mar 2 03:46:37 EST 1993


In article <9303020601.AA17760 at net.bio.net>, preissj at CLVAX1.CL.MSU.EDU ("J Preiss--Seq Anal") writes:
|> Hi
|> 
|> 	There has been some talk lately about accessing the PDB via gopher.
|> Right now, just want to find out if a given sequence has a known crystal
|> structure.  I have run FASTA of selected domains of my protein using GCG 
|> on my local VAX.  I now want to know which proteins to look up in the library
|> first.  I figure that those with known crystal structures will probably have
|> the most information about the likely structure and function of the domains
|> that I have selected.  What is the quickest way to find out this info?
|> 
|> 	Thanks
|> 
|> 	Lenny Bloksberg
|> 	PreissJ at clvax1.cl.msu.edu
|> 
|> 

You install the Sequence Retrieval System (SRS), copyrighted by Thure Etzold. 
There, you parse the FASTA file output and link it into PDB. The 
result shows you immediately which hits in the fasta output had actual 
counterparts in PDB. The fun is that you could even use a TFASTA and link 
EMBL to PDB this way. 


Another tip would be to install the NRL_3D database as provided by 
PIR International. The entries there are exclusively PDB entries. 
Running FASTA on there would give you PDB entries entirely. 

Regards
Reinhard 
 
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