A Portal for Three-dimensional Structural Information about Nucleic Acids

THE NUCLEIC ACID DATABASE NEWSLETTER

November 2003, Volume 7, Number 2


Paper Describing RNA Visualization Programs Published

Programs developed to aid in the classification and visualization of RNA are available from the NDB site at ndbserver.rutgers.edu/services/.

These programs are used to generate images of secondary structure for RNA structures in the NDB Atlas.

The BPView program is used to display the three dimensional coordinates of base pairs and base pair collections.

RNAview identifies and classifies base pair types formed in structures by various combinations of the three edges, Watson-Crick, Hoogsteen, and Sugar edge.

RNAMLview is used to rearrange the layout of the two dimensional diagrams from RNAView.

These programs are described in

"Tools for the automatic identification and classification of RNA base pairs" Huanwang Yang, Fabrice Jossinet, Neocles Leontis, Li Chen, John Westbrook, Helen Berman and Eric Westhof. Nucleic Acids Research, 2003, Vol. 31, No. 13 3450-3460

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NDB at the ACS Middle Atlantic Regional Meeting 2003

The NDB presented a poster on the NDB redesign at the ACS Middle Atlantic Regional Meeting (MARM) that was held June 8-11, 2003 at Princeton University (NJ).

As described in the last newsletter, 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. These are all available from the NDB home page at ndbserver.rutgers.edu.

"Nucleic Acid Database Redesign: Expanded Annotation and Visualization" Helen M. Berman, Chi-Ming Chao, Li Chen, Zukang Feng, Lisa Iype, Xiang-Jun Lu, Bohdan Schneider, John Westbrook, Huanwang Yang.

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NDB at RNA 2003

The NDB presented a poster on the NDB and RNA at the RNA 2003 Meeting that was held July 1-6 in Vienna, Austria.

The poster described the new Atlas features, including new molecular graphics emphasizing base pairing interactions, 2D diagrams secondary and tertiary RNA structure produced by RNAView, RNAML datafiles, and tables of hydrogen bonding, base morphology and backbone geometrical features. The new website also provides a web form for the RNAView program that allows users to upload RNA coordinate data and produce 2D diagrams of hydrogen bonding interactions and RNAML data files. A companion program RNAMLView is provided to permit the interactive editing of these 2D diagrams. The 3D structure of individual base pairs or motifs can be viewed using the new web BPViewer.

"The Nucleic Acid Database and RNA" Huanwang Yang, Fabrice Jossinet, Eric Westhof, Neocles Leontis, Bohdan Schneider, Chi-Ming Chao, Zukang Feng, Lisa Iype, Xiang-Jun Lu, Goran Aleksic, Joanna de la Cruz, Gregory Donahue, Dipannita Kalyani, Daniel Kulp, Hari Narayan, John Westbrook, and Helen M. Berman

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Review of B- and A-DNA Structures Published

Analysis of helical structures in the NDB reveals the effects of environment and sequence on DNA structure. A review of these studies and their implications on the recognition and deformability of the double helix during biologically important processes was included in a publication from the DNA50 Council. This collection intends to demonstrate the progress made since the discovery of DNA structure.
"The Many Twists of DNA". Helen M. Berman and Wilma K. Olson DNA 50: The Secret of Life. pages 104 - 124. Miriam Balaban, Editor. Published by Faircount, London. 2003.

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Paper Nucleic Acid Visualization Program Published

3DNA is used by the NDB to generate the graphics emphasizing nucleic acid features in the NDB Atlas. This program is available from the NDB site at ndbserver.rutgers.edu/services/.

"3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures" Xiang-Jun Lu and Wilma K. Olson Nucl. Acids. Res. 2003 31: 5108-5121.
http://nar.oxfordjournals.org/content/31/17/5108.abstract?etoc

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Using XML to Generate the NDB Atlas

The NDB Atlas was recently expanded and redesigned to provide pages for NMR structures; more descriptive structure categories; improved graphics, and further information about each structure.

Each entry in the NDB Atlas contains links to files for the asymmetric and biological unit coordinate files in PDB format, coordinate files in CIF format, experimental data, and images. Using a program written by the NDB, all the files needed to generate complete NDB Atlas entries are created by parsing the XML files. The XML files are created from mmCIF files generated during NDB processing.

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The Nucleic Acid Database Project is funded by the National Science Foundation and the Department of Energy.

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