October 2001 NDB Newsletter

THE NUCLEIC ACID DATABASE NEWSLETTER

October 2001, Volume 5, Number 1

1. A Standard Reference Frame for the Description of Nucleic Acid Base-Pair Geometry Published

2. NDB Chapter in International Tables Published

1. Standard Reference Frame Published

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://beta-ndb.rutgers.edu/NDB_news/ and from the Journal of Molecular Biology at http://www.idealibrary.com/links/doi/10.1006/jmbi.2001.4987/.

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 (USA).

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. grant GM20861.

2. NDB Chapter in International Tables Published

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 of Energy To subscribe or unsubscribe to the NDB newsletter, send a message to ndbnews@ndbserver.rutgers.edu.