Madison, September 20, 2000
Dear subscriber to the BMRB mailing list,
First of all let us thank each of you for your membership to the
BioMagResBank (BMRB) mailing list. We see the 100+ members on the list
so far as a vote of interest of the scientific community in a central
place for NMR specific information, and we would like to offer exactly
that.
We intend to use this mailing list to keep you up-to-date of the
services that the BMRB provides, so please encourage your colleagues to
subscribe to the list so they might benefit from our efforts. To limit
the amount of cross posting we do not intend to provide this information
on other mailing lists nor to all the authors making depositions at the
BMRB.
We draw your attention to four items on our list of newer features found
at our web site (http://bmrb.wisc.edu).
BMRB FEATURES:
1) QUERY GRID
Since August 2000, a new query system for BMRB entries allows users to
retrieve sets of BMRB entries that have defined characteristics and
content (chemical shifts, relaxation values, coupling constants, etc.
for proteins, DNA, and RNA).
2) BMRB ENTRIES MATCHED TO CORRESPONDING PDB NMR ENTRIES
The BMRB provides a list of BMRB entries matched to PDB NMR entries.
Each BMRB and PDB entry has been reviewed to confirm that the authors
and/or the citation are consistent, to determine the homology of the
biopolymer sequence between the paired entries and to compare other
characteristics of the entries including the presence of ligands, etc.
Discrepancies between the BMRB and PDB entries are noted in a comment
section. The list of matched entries will be extended continually as new
BMRB and PDB entries are released.
3) STAR FILES WITH NOES AND COORDINATES
The quality of coordinates and NOE distance constraints of 97 PDB
entries was evaluated in previous studies (Doreleijers et al.). This set
of data has now been transformed into STAR files, which follow the
latest released version of the NMR-STAR dictionary (2.1) for most data
types. The PDB entries in the current set are not yet included in the
regular BMRB database as they lack some information that was not
required for the previous studies. It is the intention of the BMRB to
provide NMR data such as constraints and coordinate information in
NMR-STAR files in the future, and we are collaborating with the RCSB to
achieve this goal.
4) DEVise DATA VISUALIZATIONS
The DEVise tool is being used to provide Chemical Shift Index (CSI,
Wishart et al.) and other plots from experimental data in BMRB entries.
DEVise is being developed by Kent Wenger and Miron Livny of the Computer
Science department here in Madison. They are currently working on a
version that will interactively display NMR experimental data together
with a three-dimensional view of the studied molecule(s). The current
DEVise "session" can be opened for each BMRB entry by selecting a button
labelled "See interactive data graphs" that is located on top of the
first data view that you will get after selecting a BMRB entry.
CURRENT CONTENT OF THE BMRB ARCHIVE:
DATA TYPE | POLYMER CLASS
| Proteins/Pep. (1621) DNA (35) RNA (9)
_________________________|____________________________________________
Chemical Shifts (all) | 450246 (1617) 4935 (31) 2874 (9)
1H | 299498 (1469) 4301 (30) 1857 (9)
13C | 110052 (415) 463 (4) 763 (4)
15N | 40840 (388) 45 (2) 235 (4)
31P | . (.) 126 (9) 19 (1)
Coupling Constants | 2572 (40) 48 (1) . (.)
T1 Values | 835 (3) . (.) . (.)
T2 Values | 851 (3) . (.) . (.)
Heteronuclear NOE Values | 956 (4) . (.) . (.)
S2 Values | 341 (3) . (.) . (.)
H-Exchange Rates | 135 (3) . (.) . (.)
H-Exchange Protection | 82 (1) . (.) . (.)
3D Structure Entries | . (1) . (.) . (.)
Values in parentheses indicate the number of entries for that category.
CRITICISM AND SUGGESTIONS:
The BMRB team and its Advisory Board welcome feedback from data
depositors and users. These may be addressed to:
John L. Markley, Head
mailto:markley@nmrfam.wisc.edu
Eldon L. Ulrich, Director
mailto:elu@bmrb.wisc.edu
Jeffrey C. Hoch, Chairman, BMRB Advisory Board
mailto:hoch@rowland.org
http://bmrb.wisc.edu/home/suggest.html
BioMagResBank STAFF
_______________________________________________________________________
|
John Markley, Head | Jurgen Doreleijers, Research Associate
mailto:markley@nmrfam.wisc.edu | mailto:jurgen@bmrb.wisc.edu
|
Eldon Ulrich, Director | Steve Mading, Scientific Programmer
mailto:elu@bmrb.wisc.edu | mailto:madings@bmrb.wisc.edu
|
| Amalia Muņoz, Associate Researcher
| mailto:amalia@bmrb.wisc.edu
_______________________________|_______________________________________
|
Ovamir Anjum, Programmer | Lei Yin, Programmer
mailto:ovamir@bmrb.wisc.edu | mailto:yleigh@bmrb.wisc.edu
|
Nancy Slatter, Annotator | Qin Zhao, Annotator
mailto:ncm@bmrb.wisc.edu | mailto:qin@bmrb.wisc.edu
|
Mike Thomas, Annotator |
mailto:mthomas@bmrb.wisc.edu |
_______________________________|_______________________________________
--
Jurgen F. Doreleijers
BioMagResBank, Univ. of Wisconsin-Madison, WI, USA
mailto:jurgen@bmrb.wisc.edu
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