A Portal for Three-dimensional Structural Information about Nucleic Acids


April 2003, Volume 7, Number 1

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://mmcif.pdb.org/index.html.

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.