A Portal for Three-dimensional Structural Information about Nucleic Acids

THE NUCLEIC ACID DATABASE NEWSLETTER

September 2002, Volume 6, Number 1



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 home page.

Your comments are greatly appreciated – please send them to ndbadmin@ndbserver.rutgers.edu.

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

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.

RNAML: http://smi-web.stanford.edu/projects/helix/pubs/rnaml/


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 ndbadmin@ndbserver.rutgers.edu.


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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NDB Article

An article describing the NDB has been published in a special issue of Acta Crystallographica B/D:

Berman, H.M., Westbrook, J., Feng, Z., Iype, L., Schneider, B., Zardecki, C. (2002): The Nucleic Acid Database. Acta Cryst. D58 889-898.

"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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