// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Volume 2. Number 2. June 1998. The NDB can be accessed through the BSR WWW site (http://ndbserver.rutgers.edu/) and its mirror sites (http://www.ebi.ac.uk/NDB/, http://ndbserver.nibh.go.jp/NDB/, http://ndb.sdsc.edu/). Comments, queries, and questions about NDB and this newsletter should be sent to ndbadmin@ndbserver.rutgers.edu. ---------------------------------------------------- Contents ---------------------------------------------------- Structure Finder: New Quick Reports Available SFCheck FREEHELIX98 Software Available mmCIF Dictionary Extensions NDB Welcomes Summer Students ---------------------------------------------------- Structure Finder: New Quick Reports Available ---------------------------------------------- Quick Report, one of the Structure Finder options, generates reports for the structures found using Quick Search. The user selects a report from the list provided and it is automatically generated. Different reports are available for each database available through Structure Finder. These reports can be printed and downloaded. Several new quick reports are available for each database, including refinement information reports, protein-only sequence reports and nucleic acid-only sequence reports. Reports available for the Structure Finder databases (http://ndbserver.rutgers.edu/NDB/structure-finder/): NDB (Nucleic acid-containing structures determined by X-ray) NDB Status, Cell Dimension, Primary Citation, Structure Identifier, Sequence, Nucleic Acid Sequence, Protein Sequence, Refinement Information, NA Backbone Torsions, Base Pair and Base Pair Step Parameters (Curves 5.1), Groove Dimensions (Curves 5.1) DNA-Binding Proteins (DNA-binding proteins determined by X-ray) Cell Dimension, Primary Citation, Structure Identifier, Sequence, Nucleic Acid Sequence, Protein Sequence, Refinement Information NMR Nucleic Acids (Nucleic acid-containing structures determined by NMR) Primary Citation, Descriptor, Sequence, Nucleic Acid Sequence, Protein Sequence Protein Plus (All structures found in the PDB) Cell Dimensions, Primary Citation, Structure Identifier, Sequence, Nucleic Acid Sequence, Protein Sequence, Experimental Technique, Refinement Information SFCheck ------- The program SFCheck (1) is now being used to check structures for which structure factor files exist. The program recomputes the R factor and correlation coefficient, gives information about data completeness and effective resolution and the local agreement between the model and the electron density map. In collaboration with Shoshana Wodak and her group in Brussels, we have analyzed the nucleic acid structures using this program. The SFCheck output for these structures can be found at ftp://ndbserver.rutgers.edu/pub/sfcheck/. (1) Alexei A. Vaguine, Jean Richelle, and Shoshana J. Wodak, Acta Crystallogr. D, in press. FREEHELIX98 ----------- The program FREEHELIX98 is now available through the NDB at ftp://ndbserver.rutgers.edu/pub/programs/freehelix98/. This directory contains operating instructions, the program in Fortran, a supplemental output routine, and sample test files. The program FREEHELIX98 is described in Dickerson, Richard E. (1998). "DNA Bending: The Prevalence of Kinkiness and the Virtues of Normality." Nucleic Acids Research 26, 1906-1926. If you have questions about how to access these files, please contact ndbadmin@ndbserver.rutgers.edu. For information about the program, please contact Dr. Richard E. Dickerson at red@biop.ox.ac.uk, or after 1 October 1998, at red@ewald.mbi.ucla.edu. mmCIF Dictionary Extensions --------------------------- Parts of this article were excerpted from the mmCIF WWW site. (http://ndbserver.rutgers.edu/mmcif/) The Nucleic Acid Database project has been actively involved in the development of the mmCIF dictionary which provides definitions of the terms needed to describe the crystallographic experiment and the results. In January 1997, the mmCIF dictionary was completed and submitted to COMCIFS for review and in June 1997, Version 1.0 was released. At the mmCIF Software Developers Workshop, held at Rutgers University in October 1997, there was much discussion about how to proceed with the maintenance and evolution of the dictionary so that it can accommodate new data items and still be compatible with existing software. The method adopted for managing these extensions uses a scientific journal as a model. The proposed extensions are sent to the Editors of the mmCIF Dictionary (Paula Fitzgerald, Editor, Helen Berman, Associate Editor) who send the new definitions to a member of the board of editors for scientific review. These editors have expertise in the various areas covered by the dictionary; they are Phil Bourne, Dale Tronrud, Andy Howard, Joel Sussman, Frank Allen and Dale Tronrud. Once the definitions are reviewed for their scientific content, they are sent to the Technical Editors, John Westbrook or Herb Bernstein. More than 100 new definitions have been proposed since the fall of 1997. Most of these were submitted by Kim Henrick as part of the efforts at the European Bioinformatics Institute in data harvesting. These have been reviewed using the procedures outlined. Version 2 of the mmCIF dictionary will contain many of these new definitions and is expected to be released the summer of 1998. NDB Welcomes Summer Students ---------------------------- We would like to welcome our new students Jason Breen (RU, '00), Tonye Briggs (Case Western University, '99), Michael Huang (RU, '99), Prasant Jagannath (Cornell, '01), Nathaniel Macapagal (RU '99), Gnanesh Patel (Swarthmore, '00) for what we hope will prove to be a very interesting summer of research! ******************************************* Researchers who wish to use information obtained from NDB should use the following citation: Helen M. Berman, Wilma K. Olson, David L. Beveridge, John Westbrook, Anke Gelbin, Tamas Demeny, Shu-Hsin Hsieh, A. R. Srinivasan and Bohdan Schneider. (1992) The Nucleic Acid Database: A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J., 63, 751-759. NDB Staff: Helen M. Berman, Director Lester Clowney, Zukang Feng, Anke Gelbin, Olivera Tosic, John Westbrook, and Christine Zardecki The Nucleic Acid Database Project is funded by the National Science Foundation and the Department of Energy // \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ //