THE NUCLEIC ACID DATABASE NEWSLETTER, June 2000, Volume 4, Number 1
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     NDB Web Site Update
     New NDB Mirror at the Institute of Cancer Research (UK)
     Tsukuba Workshop on Nucleic Acid Structure and Interactions Proceedings
     Interactions between the NDB and the PDB
     Analysis of NDB structures available


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NDB Web Site Update

The NDB Web Site has been streamlined with the Biological Structure Resource
page for our users.  The features, which include the database searches, the
mmCIF Web site, and A La Mode, are now all available from the NDB home page.
News items will also be posted.

The NDB is available at:
    http://ndbserver.rutgers.edu/	Rutgers, US
    http://ndb.sdsc.edu/		SDSC, US
    http://ndbserver.nibh.go.jp/NDB/	NIBH, Japan
    http://www.ndb.icr.ac.uk/		ICR, UK

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New NDB Mirror at the Institute of Cancer Research (UK): 
http://www.ndb.icr.ac.uk/

We are pleased to announce that the NDB is now mirrored at the
Institute of Cancer Research (ICR) in the United Kingdom at http://www.ndb.icr.ac.uk/.  
Our liaison at the ICR is Professor Stephen Neidle.

The Institute of Cancer Research, in association with the Royal Marsden
Hospital, form Europe's largest comprehensive cancer center. The
Institute is renowned for its work in the cell and molecular biology of
cancer, in cancer genetics, and in anticancer drug discovery. It has
more recently established a major new activity in structural biology.
Stephen Neidle's group at the Chester Beatty laboratories of the
Institute, is hosting the NDB mirror. His group is known for its extensive
structural studies on DNA-drug complexes, and has long had close links
with the NDB.

This site is updated regularly along with the other NDB mirrors.

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Tsukuba Workshop on Nucleic Acid Structure and Interactions

The Tsukuba Workshop on Nucleic Acid Structure and Interactions was held at
the Structural Biology Centre in Tsukuba, Japan on January 12-14, 1999.  The
meeting was funded by the COE program of the Science and Technology Agency,
Japan and the CREST program of the Japan Science and Technology
Corporation. The meeting was organized by Masashi Suzuki of the National
Institute of Bioscience and Human-Technology and Helen M. Berman and Wilma
K. Olson of the Nucleic Acid Database Project (supported by National Science
Foundation (USA).

One of the topics discussed was the finalization of the parameters
used to describe nucleic acid structure.  A resulting article, A
Standard Reference Frame for the Description of Nucleic Acid Base-Pair
Geometry, is currently available in PDF and HTML formats for review at
http://ndbserver.rutgers.edu/NDB/archives/.

Other topics discussed at the meeting included ways to describe global
features of nucleic acid structure, how best to describe the interface between
nucleic acids and proteins, and ways to describe RNA structure.

Question about this Meeting or about the article may be sent to
ndbadmin@ndbserver.rutgers.edu.

The NDB and the PDB
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The Nucleic Acid Database (NDB) began operation in 1991 as a value added
structure database containing structures determined by X-ray crystallography.
In the early operation of NDB, files deposited with the PDB were further
annotated at the NDB.  In 1992, the NDB began the processing of nucleic acid
X-ray structures deposited at PDB/BNL.  In 1996, NDB began accepting nucleic
acid structure depositions.  These structures were fully processed by NDB and
forwarded to PDB for inclusion in the PDB archive.  When the RCSB assumed the
management of the PDB in 1999, the interaction between the PDB and NDB was
simplified.  All nucleic acid structures can be found in both the NDB and PDB
and the process by which these structures are incorporated in PDB is fully
automatic.

Today all macromolecular structures can be deposited through a common
deposition system.  The sharing of deposition tools is possible
because the deposition system has been designed to provide different
views of data to different users.  The AutoDep Input Tool (ADIT; 
http://rcsb-deposit.rutgers.edu/adit/) is 
based on the same underlying architecture originally developed for
processing nucleic acid structures at NDB.  This tool presents the
depositor with a different selection of data input options depending
on macromolecule type and experiment type.  Expanded data views are
also created for annotation permitting deposition, data processing,
validation, and annotation to be performed with a common set of
software tools.

The additional annotation performed by NDB includes: characterization of the
nucleic acid chemical and biological features, intermolecular interactions,
and structural features unique to nucleic acid structures.  This information
as well as other experimental details are stored in the NDB relational
database.  This database is used to support both web-based queries and for the
production of standardized reports.  The NDB Atlas is one such summary report
which includes a concise description of the essential experimental and
chemical features of each structure along with graphic depictions of
biological assemblies and crystallographic packing interactions.

All of the extra information in the NDB can be accessed either directly from
the NDB web site (http://ndbserver.rutgers.edu) or from links provided in PDB
Structure Explorer reports produced by PDB SearchLite or SearchFields query
interfaces.

The NDB continues to develop new tools for the analysis of nucleic
acid-containing structures.  The current development focus is on the automated
assignment of secondary and tertiary structural features.  As these new
developments mature they will be made available through both NDB and PDB.

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Analysis of NDB structures available

An article that provides a detailed analysis of the DNA-binding sites of
26 proteins is presented using data from the PDB in "Protein-DNA
Interactions: A Structural Analysis" by Susan Jones, Paul van Heyningen,
Helen M. Berman, and Janet M. Thornton in the Journal of Molecular
Biology (1999) 287, 877-896.


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The Nucleic Acid Database Project Members: 
Helen M. Berman, Zukang Feng, Xiang-Jun Lu, Wilma K. Olson, Bohdan Schneider,
John Westbrook and Christine Zardecki

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.