deposition of 3d structural studies of biological macromolecules

Axel T. Brunger brunger at laplace.csb.yale.edu
Tue Dec 23 11:10:18 EST 1997


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Deposition of 3D Structural Studies of Biological Macromolecules
                  from 5-Jan-1998
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We are pleased to announce the inauguration of a new deposition site
for 3D structural studies of biological macromolecules.  Starting on
January 5, 1998, authors using the Web-based tool, AutoDep, can submit
data either to the European Bioinformatics Institute (EBI), UK or to
the Protein Data Bank (PDB) at Brookhaven National Laboratory (BNL),
USA.  The additional site is expected to significantly facilitate the
submission procedure, especially for European researchers.

AutoDep is a Web-based tool originally designed at PDB for automatic
submission of macromolecular data into the PDB.  Extensive collaboration 
between EBI and PDB has produced significant changes to the original 
system allowing for the seamless operation of multiple deposition
sites.  
This includes EBI specifications for standards and protocols to be used 
in making the code portable and generally more robust.

AutoDep is accessible from the following URLs:

        * BNL-PDB   http://www.pdb.bnl.gov
        * EBI-MSD   http://autodep.ebi.ac.uk

Those wishing to submit data using the electronic version of the
Deposition Form must continue to deposit directly to BNL using e-mail
or FTP.

The submission procedure will be identical, and equivalent, at both
sites, but PDB ID codes will be issued by BNL.  Data submitted at EBI
will be forwarded automatically to PDB after depositors have reviewed
the AutoDep-generated entry and diagnostics.  Final preparation for
archiving and release will be done by PDB staff.  We encourage
depositors 
to submit not only the structural results, but also their experimental 
data, i.e., for crystallographers, X-ray structure factors and for 
NMR spectroscopists, constraints lists and statistical data describing 
the calculated NMR conformers and constraints.

Important Notes:

 (i)   Submissions can be completed only at the site at which they were
       started. 
       
 (ii)  The option "Based on a previous submission" may be used to
simplify 
       submissions by using an earlier AutoDep session as a template. 
       However, depositors will only have access to their earlier
submissions 
       at the site where those submissions were originally made.

 (iii) Existing PDB entries may be used as templates by choosing the 
       option "Based on an existing PDB entry".  The full set of entries 
       will be available at either site, irrespective of where the
original
       deposition was made.
       
 (iv)  The date of submission for data deposited at EBI will be the
       corresponding U.S. Eastern Time of the date when submission is
       completed at EBI.
       
 (v)   EBI staff will offer assistance (via e-mail: pdbhelp at ebi.ac.uk)
up to 
       the point of submission. Once BNL has issued an ID code,
correspondence 
       should be directed to BNL (via e-mail: pdbhelp at pdb.bnl.gov).

Please note that authors should continue to deposit crystal structures
of nucleic acids to the Nucleic Acid Database (NDB) at Rutgers, the
State University of New Jersey, USA at URL:
http://ndbserver.rutgers.edu:80/NDB/deposition/index.html. 

Experimental data related to NMR studies will also be transferred
electronically to the BioMagResBank (BMRB) at the University of
Wisconsin-Madison, USA for further processing and inclusion into the
database (http://www.bmrb.wisc.edu) as well.

Joel L. Sussman                  Phil McNeil
Head, Protein Data Bank          Head, Macromolecular Structure Group
Biology Department               EMBL Outstation
Brookhaven National Laboratory   European Bioinformatics Institute
Upton, NY, USA                   Wellcome Trust Genome Campus,
                                 Hinxton, Cambridge, UK
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