From: Eldon Ulrich (elu@yola.bmrb.wisc.edu)
Date: Mon Sep 10 2001 - 09:08:59 CDT
BMRB UPDATE
Now that many of you are back from your summer holidays, we thought it would be
a good time to provide you with an update on BMRB.
Several new features are now available at the BMRB web site. Many of these
can be accessed from the 'Features' link on the BMRB home page
(http://www.bmrb.wisc.edu).
1. We are now accepting the deposition of time-domain data sets. Cheryl
Arrowsmith's group has kindly provided the first such entry. We expect to
receive a number of these entries from the structural genomics projects funded
by the NIH, but others will be welcome.
2. Interactive versions of the amino acid chemical shift histogram plots are
now available.
3. A list of PDB entries in which residual dipolar coupling restraints have been
used has been created and is being continually updated.
(http://www.bmrb.wisc.edu/dipolars/)
4. A set of standard amino acid 1H, 13C, and 15N chemical shifts derived from
peptides in 8M urea by Jane Dysan, Peter Wright and coworkers can be downloaded
in a computer parsable format. A set of chemical shift index parameters
developed by this group also is available.
http://www.bmrb.wisc.edu/ref_info/pentapeptide.tbl
5. For each protein entry, it is possible to view an interactive plot of the
chemical shift distributions for each amino acid type and also to obtain a
simulated 1H-15N 2D spectrum if the data are present in the entry. In the
1H-15N 2D spectrum, resonances can be identified by amino acid type. As an
example, try the URL below:
http://bmrb.wisc.edu/devise/peptide-cgi/data_dir/5072y.html
6. The query-grid interface for locating sets of BMRB entries containing
specific types of data has been updated to include entries containing residual
dipolar couplings.
http://www.bmrb.wisc.edu/search/query_grid/initial_grid.html
We are please to note that BMRB has crossed two significant milestones. First,
over 2000 entries are now available from the BMRB web site, representing about
700,000 chemical shifts for proteins and nucleic acids and a growing quantity of
coupling constant and relaxation data. Second, we have now received more than
1000
depositions from authors since we began soliciting direct depositions in 1996.
Christopher Dobson's group supplied the 1000th deposition. We want to thank all
of those who have taken the time to complete a BMRB deposition and the Editors
of the Journal of Biomolecular NMR, the Protein Data Bank, and the European
Bioinformatics Institute for their support and collaboration in our efforts to
obtain entries from the NMR community.
As always, we are grateful for your support and look forward to your suggestions
regarding the future development of BMRB.
Best regards,
The BMRB staff
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