The paper "A Standard Reference
Frame for the Description of Nucleic Acid Base-Pair Geometry"
has been published in the Journal of Molecular Biology
(2001; 313, pp. 229 - 237). This document is available from
the NDB at http://ndbserver.rutgers.edu/NDB_news/
and from the Journal of Molecular Biology.
The standardization of these parameters
was the subject of the Tsukuba Workshop on Nucleic Acid Structure
and Interactions that was organized by the NDB and the Structural
Biology Centre and 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
The document was prepared and made
available from the NDB for public review and discussion.
This paper is a document of the
Nomenclature Committee of IUBMB (NC-IUBMB)/IUPAC-IUBMB Joint
commission on Biochemical Nomenclature (JCBN) whose members
are R. Cammack (chairman), A. Bairoch, H.M. Berman, S. Boyce,
C.R. Cantor, K. Elliott, D. Horton, M. Kanehisa, A. Kotyk,
G.P. Moss, N. Sharon, and K.F. Tipton. The panel that prepared
this document includes Manju Bansal (Indian Institute Science,
Bangalore), Helen M. Berman (Rutgers University), Stephen
K. Burley (Rockefeller University), Richard E. Dickerson (University
of California, Los Angeles), Mark Gerstein (Yale University),
Stephen C. Harvey (University of Alabama at Birmingham), Udo
Heinemann (Max-Delbruck-Centrum), Stephen Neidle (Institute
of Cancer Research), Xiang-Jun Lu (Rutgers University), Wilma
K. Olson (Rutgers University), Zippora Shakked (Weizmann Institute),
Heinz Sklenar (Max-Delbruck-Centrum), Masashi Suzuki (AIST-NIBHT
Structural Biology Centre), Chang-Shung Tung (Los Alamos National
Laboratory), Eric Westhof (Strasbourg), and Cynthia Wolberger
(Johns Hopkins University). The survey of small molecule crystal
structures was performed by John Westbrook (Rutgers) and Helen
M. Berman. The optimization of standard base-pair geometry
and the calculation of derived parameters were carried out
by Xiang-Jun Lu and Wilma K. Olson with support from U.S.P.H.S.
2. NDB Chapter in International Tables
A chapter describing the NDB has
been published in the International Tables for Crystallography
(Volume F: Crystallography of Biological macromolecules. Editors:
M.G. Rossmann and E. Arnold, 2001. Cordrecht: Kluwer Academic
Publishers, The Netherlands). "The Nucleic Acid Database"
describes the contents of the database, data processing procedures,
and how the resource is used. Further information about the
International Tables is available from the IUCr at http://www.iucr.ac.uk/iucr-top/it/index.html.
The Nucleic Acid Database Project Members:
Helen M. Berman, Zukang Feng, Lisa Iype, 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
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