// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Number 16. October 1995. Dear Friends and Users of NDB, The NDB is now almost five years old. Through the years, the database has grown in both quantity and in quality. We started with less than 100 DNA/RNA crystal structures, and now have close to 400 nucleic acid-containing structures. NDB Holdings as of October 31, 1995 408 Structures (390 released) A-DNA 51 DNA/RNA 11 A-RNA 10 DNA-Drug 93 B-DNA 66 RNA-Drug 19 Z-DNA 47 t-RNA 10 Unusual DNA 21 Protein-Nucleic Acids 66 Unusual RNA 14 Summarized here are the various services offered by the NDB Project. --------------- World Wide Web: --------------- Have you surfed over to the NDB homepage on the World Wide Web yet? If you point your browser at http://ndbserver.rutgers.edu you will discover our new look and the new services that we have been developing. These include: Searching the NDB Database: ------------------------ Click on the pointer at the top of the home page and you will be able to search the Nucleic Acid Database via a convenient APPLICATION INTERFACE PROGRAM. You may search for structures based on a variety of structural and experimental characteristics stored in the NDB. From the resulting list of structures, you can select an output format from our various options: the coordinates in NDB or PDB format; the full NDB entry; the molecular structure using either a local viewer or a remote viewer (RasMol); or the full Atlas entry. TUTORIALS are also available on the server to provide assistance and to get you started searching. NDB Archives: ------------ In the NDB ARCHIVES, you will find NDB output reports about all the structures in the NDB. The reports include citations, structural features and cell dimensions. There are also tables of protein-nucleic acid structures, tRNA structures, and structures with bound drugs, modified phosphates, modified bases and mismatches. These are the same reports that have always been available via our electronic file server, and are updated with each newsletter release. From now on, we will update these reports monthly. Please note that these reports are only example reports, and that the NDB staff can provide you with any kind of report, including graphs based on the contents of the database or special searches upon request. Also contained in the archives are all of our newsletters, the NDBquery manual, the ftp site, bibliographies of review articles, and bibliographies of research articles that cite the NDB. *Nucleic Acid Dictionaries: A special feature of the NDB archives is the new Nucleic Acid Dictionaries section. The NDB project has derived distances and angles for the sugars, bases, and phosphates using high resolution (less than 1.0 Angstrom) crystal structures. The parameter and topology files for use with X-PLOR are in this Nucleic Acid Dictionaries section of the Archives. Standard coordinate sets and dictionaries for other programs are being prepared. A paper describing how these parameters were derived is in press: "New Parameters for the Refinement of Nucleic Acid-Containing Structures" by Gary Parkinson, Jaroslav Vojtechovsky, Lester Clowney, Axel T. Brunger, and Helen M. Berman will be published in Acta Cryst. D. NDB Atlas: ---------- We are also pleased to present the NDB ATLAS of Selected NDB Structures. This Atlas was originally created with the assistance of undergraduate students here at Rutgers University. Each Atlas "page" highlights the bibliographical, structural and experimental information about each structure, includes pictures from different views and is linked to the structure's coordinate file. Each Atlas page is now created directly from NDBQUERY. All structures will soon be available in the Atlas as a result of this feature. Collaboration with mmCIF: -------------------------- The NDB project has been working closely with the Macromolecular Crystallographic Information File (mmCIF) Project. The NDB project has employed mmCIF as an interchange format using a locally developed dictionary. At each stage in the evolution of the mmCIF dictionary, software tools have been developed by the NDB to evaluate the extent to which each dictionary would facilitate the automated processing of data. The result of this development is the collection of software tools called SIFLIB. If you want to learn more about the Macromolecular Structure Dictionary Description Language (DDL), the mmCIF dictionary, SIFLIB, or view examples, please explore the DDL and mmCIF homepages that are featured on the NDB homepage. General Information: -------------------- The section GENERAL INFORMATION on our homepage provides subscription and query information for NDB that is also provided in our newsletter. Also found in this section are important links to other databases and biochemical research centers. If you have a suggestion for a link, please let us know. ---------------------- Validation Project ---------------------- The NDB group has been creating new validation tools for nucleic acid structures. The first step was to create new dictionaries for the valence geometry. Tools for evaluation of these parameters as well as for the valence geometry, torsion angles, and base morphology parameters are being created and will be made available soon. --------- Meetings: --------- The latest developments of the NDB project were presented at several meetings this summer: at the Ninth Conversation for Biomolecular Stereodynamics, in Albany, NY, in June; at the conference entitled "Towards a Federation of Macromolecular Databases" sponsored by the Committee on Data for Science and Technology (CODATA), in Fairfax, VA, in June; at the annual meeting of the American Crystallographic Association, Montreal, Canada, in July; and at the Workshop on Crystallographic Databases at the National Institute for Standards and Technology, Gaithersburg, MD, in August. ----------------------------- Questions, Comments, Queries: ----------------------------- Specialized and custom queries that are not yet available through the forms- based interface on the WWW may be requested by sending mail to ndbadmin@ndbserver.rutgers.edu. These requests can be for tabular reports containing general bibliographic, structural and experimental information, as well as the derived quantities available in the database, which include bond lengths, valence angles, torsion angles, and base morphology parameters. Molecular graphics, including packing pictures, may also be requested. ---------------------------------- SUMMARY OF NDB ACCESS INFORMATION: ---------------------------------- E-mail: To: ndblib@ndbserver.rutgers.edu Subject: send access from newsletter Anonymous ftp: ftp ndbserver.rutgers.edu World Wide Web: http://ndbserver.rutgers.edu ----------------- ACKNOWLEDGEMENTS: ----------------- We would like to congratulate Jim Sloan from the Department of Biochemisty at the University of Washington for winning our unofficial "design our new newsletter logo" contest. Thanks Jim! 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. The Nucleic Acid Database Project is funded by the Division of Instrumentation and Resources of the National Science Foundation (BIR 9305135).