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
