Beta Test New NDB Site - http://beta-ndb.rutgers.edu/
The NDB Project has redesigned the NDB Web site and has made it
available for beta testing by our user community. This beta site will
be used to present new developments for feedback before they are
integrated into the current NDB site. The beta NDB Web site
(http://beta-ndb.rutgers.edu/) will be linked to from the current NDB
Your comments are greatly appreciated please send them to
The main NDB site and its mirrors will continue to be updated on a
regular basis, and should be used when looking for newly released
structures. The last update of the beta site will be indicated on the
home page. Information about unreleased structures will not be made
available from the beta site at this time.
The features of the NDB redesign include a new look and layout, a
greatly revised new Atlas, a new database that includes X-ray and NMR
structures, and a new search engine.
Redesigned Look and Layout
The new NDB site graphics and layout have been created to enhance
navigation through the site. There are eight main sections Atlas,
Deposit, Download, Search, Reports, Education, Standards, and Links
available from the navigation link at the top of most NDB pages. A
site index shows the entire NDB site at a glance.
|Atlas:||Summary information and graphics for all NDB structures|
|Deposit:||Information on depositing structures to the NDB|
|Download:||Download coordinates and more from the FTP server|
|Search:||Queries and reports on the NDB|
|Reports:||Prepared summary reports on the NDB holdings|
|Education:||An introduction to nucleic acids|
|Standards:||Nucleic acid standards|
|Links:||Links to a variety of related resources|
The expansion and redesign of the NDB Atlas includes: pages for NMR
structures; more descriptive structure categories; improved graphics, and
further information about each structure.
The Atlas is divided into X-ray and NMR structures at the top level,
and then is divided into further categories (such as DNA Junctions and
Viruses). The top level page for each category includes images for each
structure listed. A text only option is also available.
These images are part of the new graphics used at this site. Pictures
which emphasize nucleic acid features were created by 3DNA software
(Xiang-Jun Lu and Wilma Olson, Rutgers). Secondary structure pictures
are now available for RNA structures. These pictures were created by
software developed by Huanwang Yang (Rutgers) in collaboration with
Fabrice Jossinet (CNRS), N. Leontis (Bowling Green University), and
Eric Westhof (CNRS). RNAML files which were used to create the RNA
pictures can also be downloaded.
Links to structure factor files and links to tables of derivative data
are now available. Derivative data tables include nucleic acid
backbone torsions, base pair parameters, base pair step parameters,
and hydrogen bonding classification. Base pair and base pair step
parameters are based on A Standard Reference Frame for the Description
of Nucleic Acid Base-pair Geometry (Olson et al., Journal of Molecular
Biology (2001) 313: 229 - 237). Hydrogen bonding classifications
based on the Saenger classification (Saenger) and based on the
Leontis/Westhof classification (Leontis and Westhof, RNA (2001) 7:499
- 512) are present.
New Database: X-ray and NMR Structures
Nucleic acid-containing structures determined by NMR are now included
in the new database and in the Atlas Section of the beta NDB site.
The new database is based upon the PDB mmCIF Extension Dictionary
available from http://mmcif.pdb.org/index.html.
New NDB Search Engine
The new Search page available on the beta NDB site is an extended
version of the Quick Search page on the current NDB site. The new
search allows queries of X-ray structures, NMR structures, or
both. Query fields are divided into categories: General Information,
Experimental Type, Sequence, Biomolecule, Nucleic Acid Modifications,
and Structural Features. The Search page is being updated on a regular
basis and new query fields will be activated once they have been tested.
Once a search results set is obtained, users have two choices. First,
users can click on an ID in the results set which will direct them to
the Atlas page for the entry. Second, users can select IDs of
interest and generate pre-defined reports for information such as
Base Pair Parameters.
This search engine will be further developed based upon user feedback.
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Be a Beta Tester!
We look forward to all comments on the new NDB site at
http://beta-ndb.rutgers.edu/ please send them to
NDB Summer 2002 Internship Program
The NDB is particularly excited about the new Atlas available from the
beta site. This Atlas was generated due to the extraordinary
efforts of the students participating in the NDB Summer 2002
Internship Program: Goran Aleksic (Rutgers College, 2004), Joanna de
la Cruz (Rutgers College, 2003), Gregory Donahue (Rutgers College,
2003), Dipannita Kalyani (Bryn Mawr College, 2003), Dan Kulp (Rutgers
University College, 2004), and Hari Narayan (Rutgers College, 2004).
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An article describing the NDB has been published in a special issue of Acta
Berman, H.M., Westbrook, J., Feng, Z., Iype, L., Schneider, B.,
Zardecki, C. (2002): The Nucleic Acid Database. Acta Cryst.
"The Nucleic Acid Database" describes the contents of the database,
data processing procedures, and how the resource is used.
NDB at IUCr Congress and General Assembly
The NDB presented a poster "Nucleic
Acid Database: New Features" that described the new features
of the NDB at the XIX Congress and General Assembly of the
International Union of Crystallography in Geneva, Switzerland
(August 6-15, 2002). Thanks to everyone who stopped by.
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The Nucleic Acid Database Project Members
Helen M. Berman, Zukang Feng, Lisa Iype, Xiang-Jun Lu, Wilma K. Olson,
Bohdan Schneider, John Westbrook, Huanwang Yang and Christine Zardecki
NDB Summer 2002 Atlas Project: Goran Aleksic, Joanna de la Cruz,
Gregory Donahue, Dipannita Kalyani, Dan Kulp, Hari Narayan
The Nucleic Acid Database Project is funded by the
National Science Foundation and the Department of Energy.
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