// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Number 18. April 1996. -------------------------- The Nucleic Acid Database (NDB) is now mirrored at The European Bioinformatics Institute (EBI) -------------------------- The NDB World Wide Web site is now being mirrored at the European Bioinformatics Institute at http://www.ebi.ac.uk/NDB/. We encourage our European users to visit this location soon. When you visit the NDB using either the original address (http://ndbserver.rutgers.edu) or the mirror site, you will see the many new developments that are summarized below. -------------- NDB on the WWW -------------- *NEW* WWW Interface to the NDB Database v. 3.0 The latest version of the NDB WWW Query Interface provides several new options for using the database, including a full structure selection and report generation interface, a simple structure selection form for making quick selections, and a simple form interface for receiving status reports on the NDB holdings. *NDB FULL QUERY INTERFACE* After selecting a set of structures, the NDB Full Query Interface provides the user with several output options. Structures may be viewed in the mmCIF format, the NDB Atlas format, the NDB coordinate format, or the PDB coordinate format. With this new interface, tabular reports can also be generated to highlight the information of interest to the user. Examples of reports produced in this manner are provided in the Archives section. *NDB QUICK SEARCH* The NDB Quick Search provides a simple form interface which enables the selection of structures according to their structural and crystallographic features. *NDB STATUS REPORT* The NDB Status Report interface allows the user to make a status report for NDB structures by selecting the structure identifier code, the name of a depositing author, the title of the structure, or the status code. Tutorials to using these interfaces are also available via the WWW. We are very interested in getting your feedback, so if you have questions about this Interface, or if you uncover a bug, please let us know by sending mail to ndbadmin@ndbserver.rutgers.edu. ------------------------------ *NEW*Nucleic Acid Dictionaries ------------------------------ *X-PLOR Parameters* 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 available on our WWW server, and a paper describing how these parameters were derived appeared in Acta Cryst. D. "New Parameters for the Refinement of Nucleic Acid-Containing Structures" Gary Parkinson, Jaroslav Vojtechovsky, Lester Clowney, Axel Brunger, and Helen M. Berman. (1996) 52, 57-64. *Valence Geometries* The Archives section of our WWW site now contains supplementary materials for surveys recently published in the Journal of the American Chemical Society. These new parameters serve as a basis for a dictionary of standard nucleic acid geometry. "Geometric Parameters in Nucleic Acids: Sugar Phosphate Constituents" describes a statistical survey of well-refined mononucleoside, mononucleotide, dinucleoside monophosphate, and trinucleoside diphosphate crystal structures found in the Cambridge Structural Database and the Nucleic Acid Database. (Anke Gelbin, Bohdan Schneider, Lester Clowney, Shu-Hsin Hsieh, Wilma K. Olson, and Helen M. Berman. "Geometric Parameters in Nucleic Acids: Sugar Phosphate Constituents" (1996) J. Am. Chem. Soc. 118, 519-529.) The WWW site contains tables of the mean values and the estimated standard deviation for the bond lengths, angles, and torsion angles in furnaose rings and in the phophodiester linkage in dinucleoside monophosphates and trinucleoside diphosphates; and the references for the structures used in the study. "Geometric Parameters in Nucleic Acids: Nitrogenous Bases" describes a statistical survey of small molecules found in the Cambridge Structural Database for high-resolution X-ray and neutron crystal structures. (Lester Clowney, Shri C. Jain, A. R. Srinivasan, John Westbrook, Wilma K. Olson, and Helen M. Berman. (1996) J. Am. Chem. Soc. 118, 519-529.) Tables of the mean values and the estimated standard deviation for the bond lengths, angles, and torsion angles for cytosine, protonated cytosine, thymine, uracil, adenine, protonated adenine, and guanine, and the references for the structures used in the study, are also available at this site. ---------- *NEW*mmCIF ---------- The NDB Project has been closely involved with the development of the Macromolecular Crystallographic Information File (mmCIF). Information about this project is available at the NDB site, and includes background information, mmCIF dictionaries, mmCIF examples, DDL information, mmCIF software tools, the mmCIF mailing list, and references. Please explore these pages to see the latest mmCIF information. ------------ NDB Holdings ------------ 426 Structures as of April 2, 1996 B-DNA 59 A-DNA 53 Z-DNA 47 A-RNA 10 DNA/RNA Hybrid 12 DNA Drug 97 RNA Drug 19 tRNA 10 Protein-Nucleic Acids 70 Unusual Nucleic Acids 49 -------------- Other Services -------------- Deposition. As of January 1, 1996, NDB has been the direct deposition site for crystal structures of oligonucleotides. Deposition information is available on the WWW site, our ftp server, and by contacting deposit@ndbserver.rutgers.edu Atlas. Our Atlas of Selected Nucleic Acid Structures is constantly growing. Each Atlas entry highlights the bibliographical, structural and experimental information about each structure and includes graphics and coordinates. Access. World Wide Web: http://ndbserver.rutgers.edu mirrored at: http://www.ebi.ac.uk/NDB/ Anonymous ftp: ftp ndbserver.rutgers.edu Electronic Library: To: ndblib@ndbserver.rutgers.edu Subject: get index Comments, queries, and questions about NDB and this newsletter should be sent to ndbadmin@ndbserver.rutgers.edu. 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 // \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ //