UPDATE: EMBL-EBI Macromolecular Structure Database and the PDB
http://msd.ebi.ac.uk
1. GLASGOW IUCr MEETING
If you are at the Glasgow meeting, you are welcome to visit our stand (5-9
August) and to attend the information session starting at 12:00 on 11th
August.
2. DEPOSITION OF NEW STRUCTURES TO PDB AT EBI
You may deposit structures to the PDB using AutoDep at EBI
( http://autodep.ebi.ac.uk ). If you need help completing the forms, please
email pdbhelp at ebi.ac.uk. We will normally reply quickly during 09:00-17:00
GMT working hours. A PDB ID code will be issued by email as soon as the
AutoDep session is completed.
WHO PROCESSES DEPOSITIONS MADE AT EBI?
All depositions made at EBI since 15th June 1999 have been processed by EBI-
MSD staff. Entries that have been reviewed by the authors and reached their
release date are forwarded each Monday to the RCSB for general distribution
through the ftp site on Wednesday.
WHAT IS THE FUTURE OF AUTODEP AT EBI?
EBI-MSD is developing a new system for the management of data on the three
dimensional structure of macromolecules. The deposition interface to this
system will be phased-in starting in the Autumn of 1999. A demonstration of
the new deposition system will be made at the IUCr Glasgow conference.
DEPOSITIONS IN THE USA
You can deposit to the PDB at the RCSB using the ADIT system
(http://pdb.rutgers.edu). RCSB are also supporting AutoDep for continuing
submissions started at Brookhaven National Laboratory. Data submitted to the
USA site are processed by the RCSB.
DOES IT MAKE ANY DIFFERENCE WHERE I DEPOSIT MY DATA?
No. EBI-MSD and RCSB work closely to maintain consistent data processing
procedures. You should choose the deposition site that is most convenient
for
your time zone.
3. QUERYING THE PDB
There are a very large number of services on the WWW that provide access to
the PDB and data derived from it. In this section we only mention tools that
are directly related to the EBI-MSD, the former PDB at BNL and the RCSB.
3DB BROWSER
EBI-MSD are continuing to support querying of the PDB by the tools
http://www2.ebi.ac.uk/pdb-bin/pdbmain and
http://www2.ebi.ac.uk/pdb-bin/pdblite. However, we are not enhancing or
developing them.
NEW EBI-MSD TOOLS
Extensive work at EBI on clean-up of the legacy PDB files has led to the
development of the following services:
PQS http://msd.ebi.ac.uk/Services/Quaternary/quaternary.html provides
access to the probable quaternary structures of macromolecules.
3Dseq http://msd.ebi.ac.uk/Services/Sequence/sequence.html provides a
direct mapping between the PDB and SWISS-PROT sequence database at the
residue level. Residue differences are annotated.
Unpublished References
http://msd.ebi.ac.uk/Services/UnPubRef/unpubref.html provides links to
references for structures listed as Unpublished.
New search tools are under development by the EBI-MSD project and these will
be announced as they become available.
NEW RCSB SEARCH TOOLS
The RCSB offer a range of search tools. Please see
http://www.rcsb.org/pdb/searchlite.html for information.
4. PDB FTP SITE AT EBI
The RCSB maintain the ftp site that contains PDB format data files. At EBI
we
provide a full mirror (ftp://ftp.ebi.ac.uk/pub/databases/pdb) of this site
in
the same form as it was maintained by the former PDB at BNL. We will shortly
also support a new simplified RCSB ftp site structure.
5. FEEDBACK
If you believe you have found a problem with a released PDB entry, or have
any questions or suggestions about EBI-MSD services, then please let us know
by email to: pdbhelp at ebi.ac.uk.
------------
Geoff Barton, EMBL-European Bioinformatics Institute, Genome Campus,
Hinxton, Cambs CB10 1SD, U.K., mailto:geoff at ebi.ac.ukhttp://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496
http://msd.ebi.ac.uk, EMBL-EBI Macromolecular Structure Database
