quick title search of PDB

Dan Jacobson danj at welchgate.welch.jhu.edu
Tue Mar 2 11:17:19 EST 1993


Newsgroups: bionet.software
Subject: Re: quick title search of PDB
References: <9303020601.AA17760 at net.bio.net>
Distribution: bionet
Organization: Johns Hopkins Univ. Welch Medical Library

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
>
>

Probably the easiest way to do this is to use the mailserver at PIR to do
as Fasta search of NRL_3D.  Once you see the results of that search you can 
retrieve the full  NRL_3D and PDB entries by gopher at merlot.welch.jhu.edu 
as discussed earlier.  Below is information extracted from a post by John
Garavelli on how to do a Fasta search of NRL_3D via the PIR mailserver.

----------

The following is extracted from the Announcements of the Protein Information
Resource Network Request Service published last summer.
 5. FASTA Searches for NRL_3D Only
 Some users had suggested that they wanted to do FASTA sequence searches
 only for the sequences with known 3-dimensional structures, the sequences
 extracted from the Brookhaven Protein Data Bank in NRL_3D.  Normally our
 FASTA searches are done against all the protein databases, PIR1, PIR2, PIR3,
 the non-redundant PATCHX (described in the August announcement and in part 2
 above) and NRL_3D.  Now when the command
   USE BASES NRL_3D
 is used before a SEARCH command, only the NRL_3D database will be used for
 the FASTA search.  Otherwise, all the protein databases will be used.

To do the search you want, send an electronic mail message containing
the following lines (with the appropiate sequence substitution)
  USE BASES NRL_3D
  SEARCH protein_sequence_in_single_letter_code
to the PIR Network Request Service address FILESERV at NBRF.Georgetown.EDU on
Internet or FILESERV at GUNBRF on BITNET.  The server will return the result of a
FASTA search through only the protein sequences with reported atomic positions
in the Brookhaven Protein Data Bank.  The first four characters of the entry
codes in the NRL_3D database correspond to the PDB entry codes.  [ . . . ]

Addition information can be obtained by sending a HELP request to the PIR
Network Request Service address.
--------------------------


Best of luck,

Dan Jacobson

danj at welchgate.welch.jhu.edu




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