*Brookhaven Protein Structure Database

Dan Jacobson DANJ at JHUHYG.bitnet
Sun Dec 1 16:20:27 EST 1991


A request was made for an ftp site for the Brookhaven database (PDB).  I don't
know of a anonymous ftp site as yet but the PDB is on the EMBL net
server.  As EMBL is scheduled to switch over to internet and (I believe) become
an ftp site soon, it will probably be ftp'able from there in the not to distant
future.  Until then the following is a description of the PDB as available from
NETSERV at EMBL.

Happy Hunting,

Dan Jacobson
danj at jhuhyg.sph.jhu.edu  (internet)
danj at jhuhyg              (bitnet)

===============================================================================

Comments: ------------
Comments: Please note:
Comments: The EMBL withdraws from Bitnet on 31-Dec-1991.
Comments: After that date, EMBL will only be reachable at the Internet address:
Comments: EMBL-Heidelberg.DE
Comments: ------------

HELP PROTEINDATA  [DIR PROTEINDATA]


The service provided by the EMBL Data Library, Computer Group and
Protein Design Group allows users to download the files constituting
the Brookhaven protein structure database and related information.

Files from this directory can be obtained by sending the command
GET PROTEINDATA:filename
to the file server.


The following files are available in the ProteinData directory:

     o    Protein Data Bank (Brookhaven) coordinate entries

          BRK.DIR         - list of BRK entry names
          BRKNEW.DIR      - list of new/changed entries in latest release
          BROOKDIR.DOC    - header records for each BRK entry
          OBSLTE.DOC      - list of obsolete entries
          protein.BRK     - structure coordinates
          protein.BRK_MOD - model structure coordinates
          NEWSLETTER.DOC  - latest PDB Newsletter
          NEWSLETTER.47 to NEWSLETTER.56   - NewsLetter (previous issues)

          examples: get PROTEINDATA:BROOKDIR.DOC
                    get PROTEINDATA:2SEC.BRK

     o    Coordinates of protein structures determined by x-ray
          crystallography at EMBL, in Brookhaven format.

          ROP2.BRK - rop wild type refined structure

          example: get PROTEINDATA:ROP2.BRK

     o    Secondary structure digest of Protein Data Bank (Brookhaven)
          protein files, derived by a pattern recognition
          program DSSP (Definition of Protein Secondary Structure).

          The protein.DSSP files only exist if the entry is for a
          protein, and at least the backbone coordinates are known.

          DSSP.DIR      - list of DSSP filenames
          protein.DSSP  - secondary structure for one protein

          example: get PROTEINDATA:1MBN.DSSP

     o    Database of homology-derived protein structures
          alias: database of protein families
          alias: database of multiple sequence alignments
          One file for each PDB protein.

          Associated utility programs in source code for VMS or UNIX:

          HSSP.DIR              - list of HSSP filenames
          protein.HSSP          - secondary structure for one protein
          filter_hssp.for       - filters a sequence family by your own criteria
          metric-gcg.data       - exchange matrix required for filter_hssp
          find_hssp.com         - finds a protein sequence in the database
          find_hssp.csh         - table for use with find_hssp
          hssp_swissprot.table
          hssp_to_insight.for   - prepares coloring by variability in 3D
          hssp_to_sybyl.for
          read_hssp.for         - reads HSSP files

          example: get PROTEINDATA:1PPT.HSSP

     o    Model coordinates from the 1986 and 1990 EMBO courses on
          protein design.

          TINY.BRK_MOD - tiny TIM
          BABA.BRK_MOD - babarellin
          BEAL.BRK_MOD - betaalphacin
          BUND.BRK_MOD - bundle
          FXNM.BRK_MOD - mutated flavodoxin
          FXNI.BRK_MOD - idealized flavodoxin
          RCU1.BRK_MOD - copper-binding rop

          GRENDEL.BRK_MOD - 4-helix membrane anchor
          FINGERCLASP.BRK_MOD - dimer of interdigitating beta-beta-alpha units
          SHPILKA.BRK_MOD - four-on-four antiparallel beta sandwich
          AIDA.BRK_MOD - designed anti-flavodoxin antibody
          LEATHER.BRK_MOD - minimal NAD binding domain

          example: get PROTEINDATA:TINY.BRK_MOD



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