THE NUCLEIC ACID DATABASE NEWSLETTER
April 2003, Volume 7, Number 1
After a period of community testing through its beta test site, the
NDB Project is launching its redesigned website.
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.
New AtlasThe 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.
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
User comments on this beta search engine should be sent to firstname.lastname@example.org.
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.
An article describing the NDB has been published:
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