Release of the Updated and Expanded NDB Website - http://ndbserver.rutgers.edu
After a period of community testing through its beta test site, the
NDB Project is launching its redesigned website.
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 nine main sections -- Atlas,
Deposit, Download, Search, Reports, Education, Standards, Tools 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 |
| Tools: | Web programs and downloadable software |
| Links: | Links to a variety of related resources |
New Atlas
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.
Much of the NDB Atlas reengineering work done was done as part of the
NDB Summer Research Project (2002) where undergraduate students from
Bryn Mawr College and Rutgers worked closely with the NDB staff.
RNAML: http://smi-web.stanford.edu/projects/helix/pubs/rnaml/
New beta NDB Search Engine and Database
In addition to the regular NDB query and reporting options, a new beta
NDB Search tool is available to query a new database that contains
nucleic acid containing structures from NMR and X-ray crystallographic
studies.
The new database is based upon the PDB mmCIF Extension Dictionary
available from http://deposit.pdb.org/mmcif/.
The new beta 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. This beta Search page is
currently under development. 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.
User comments on this beta search engine should be sent to
ndbadmin@ndbserver.rutgers.edu.
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DNA Day Resources
April 25, 2003 marks the 50th anniversary of the publication of the
description of the structure of the double helix. Teachers and
students are encouraged to celebrate these historic achievements on
this "DNA Day". Many web sites have compiled a wealth of information
about this event -- a few are listed below.
The National Human Genome Research Institute (http://www.genome.gov/)
has a variety of teaching resources for National DNA Day at
http://www.genome.gov/10506367.
The Nature Publishing Group has compiled the original articles,
historical perspectives, and examinations of DNA in medicine,
society, and as a biological molecule in "Double Helix: 50 years of
DNA" at http://www.nature.com/nature/dna50/.
The Cold Spring Harbor Laboratory has a Celebration of 50 Years of DNA
at http://www.dna50.org/, which provides resources and a schedule of
events around the world.
The 50th Anniversary Conference (on April 25) and other
resources from the University of Cambridge are available at
http://www.admin.cam.ac.uk/univ/science/dna/
King's College is sponsoring A Day of Celebrations on April 22 with
DNA information at http://www.kcl.ac.uk/depsta/ppro/dna/
Other 50th anniversary events, including articles and meetings, are
included at http://www.dna50.org.uk/.
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NDB Article
An article describing the NDB has been published:
Berman, HM, Westbrook, J, Feng, Z, Iype, L, Schneider, B, Zardecki, C
(2003). The Nucleic Acid Database. Structural
Bioinformatics. P. E. Bourne and H. Weissig. Hoboken, NJ, John
Wiley & Sons, Inc.: 119-216.
"The Nucleic Acid Database" describes the contents of the database,
data processing procedures, and how the resource can be used.
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The Nucleic Acid Database Project Members
Helen M. Berman, Joanna de la Cruz, Zukang Feng, Lisa Iype, Wilma K. Olson,
Bohdan Schneider, John Westbrook, Huanwang Yang and Christine Zardecki
NDB Summer 2002 Atlas Project: Lisa Iype, 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.
To subscribe or unsubscribe to the NDB newsletter, send a message to
ndbnews@ndbserver.rutgers.edu.
