// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Number 20. December 1996. All of the NDB developments and projects discussed in this newsletter are available through the WWW site (http://ndbserver.rutgers.edu) and its mirror at the European Bioinformatics Institute (http://www.ebi.ac.uk/NDB/). Comments, queries, and questions about NDB and this newsletter should be sent to ndbadmin@ndbserver.rutgers.edu. *** CONTENTS Season's Greetings NDB Welcomes Zukang Feng Conference and Workshop Reports Development of NDB Mirror in Japan Data Deposition and Processing Recent Publications *** ------------------ Season's Greetings ------------------ Happy Holidays from all of us at NDB! + "X" "XXX" "XXXXX" "GOD JUL" "BUON ANNO" "FELIZ NATAL" "JOYEUX NOEL" "VESELE VANOCE" "MELE KALIKIMAKA" "NODLAG SONA DHUIT" "BLWYDDYN NEWYDD DDA" """""""BOAS FESTAS""""""" "FELIZ NAVIDAD" "MERRY CHRISTMAS" "KALA CHRISTOUGENA" "VROLIJK KERSTFEEST" "FROHLICHE WEIHNACHTEN" "BUON NATALE-GODT NYTAR" "HUAN YING SHENG TAN CHIEH" "WESOLYCH SWIAT-SRETAN BOZIC" "MOADIM LESIMHA-LINKSMU KALEDU" "HAUSKAA JOULUA-AID SAID MOUBARK" """""""'N PRETTIG KERSTMIS""""""" """""""""""""""""""""""""""""""""""""" XXXXX XXXXX XXXXX >From Mike Jittlov XXXXXXXXXXXXX ------------------------ NDB Welcomes Zukang Feng ------------------------ The NDB would like to take this opportunity to welcome Dr. Zukang Feng as the newest addition to our team. Zukang, who brings to the NDB his background in computational molecular biology, will be working on new validation projects. We wish Shu-Hsin Hsieh, who has worked with the NDB for the past six years, the best of luck in her new position. ------------------------------- Conference and Workshop Reports ------------------------------- John Westbrook recently attended the Protein Ligand Database Workshop at the European Bioinformatics Institute where he described the NDB's on-going work in the development of automated tools for constructing dictionaries of high resolution crystallographic models for polymer and nonpolymer components of nucleic acid and protein systems. These dictionaries are expressed using the data representation of the mmCIF dictionary (http://ndbserver.rutgers.edu/NDB/mmCIF). In this dictionary, representations of model geometries are fully integrated with the description of the final crystallographic structure. It is our hope that providing and maintaining dictionaries of model geometries derived from high resolution small molecule experiments will be useful to both producers and consumers of macromolecular crystallographic structures. Helen Berman and Wilma Olson recently presented talks on the NDB at the 24th Aharon Katzir-Katchalsky Conference in Jerusalem. The meeting was held in celebration of the 25th anniversary of the Protein Data Bank and the 10th anniversary of Swiss-Prot. It was a lively conference that provided the attendees with an opportunity to exchange ideas about the merging worlds of structure and bioinformatics. ---------------------------------------------------------------------------- Development of New Mirror at the AIST-NIBHT Structural Biology Centre, Japan ---------------------------------------------------------------------------- Beginning in January, 1997, the NDB will begin the development of a new mirror of the Nucleic Acid Database WWW site in Japan. Thanks to the help of Professor Masahi Suzuki and the AIST-NIBHT at the Structural Biology Centre in Higashi, the NDB will have a server site in Japan. The Japan mirror will supplement our existing mirror site at the EBI and the NDB home site at Rutgers University. A formal announcement with address information will be made in mid-January. ------------------------------ Data Deposition and Processing ------------------------------ January 1, 1997 marks the first anniversary of NDB's status as the direct deposition site for the crystal structures of oligonucleotides. We have enjoyed working with the depositors, and are please to report that our average time from deposition to release is less than one month. Our procedures for data processing are summarized below: * All data are deposited electronically and processed using a template structured according to the Macromolecular Crystallographic Information File (mmCIF; http://ndbserver.rutgers.edu/mmcif/). This allows us to include information about the crystallographic experiment and structural features in processing. * The use of mmCIF also allows for automatic checking of the relationships among data items, such as sequence and coordinates. After the data have been subjected to this first round of checking, they are entered into the database and their geometrical features are validated. This involves checking the distances and angles against standard dictionaries, reviewing the torsion angles, and comparing them with ranges of values contained in similar structures in the archive, and checking the intermolecular contacts. * Structure validation is done by utilizing the reporting functions of the NDB. For example, the NDB Atlas page highlights information about a structure in a compact presentation and includes graphical representations of the biological unit and the crystal packing. * After all checks have been done, the program MaxIT (Macromolecular Exchange Input Tool; Technical Report NDB-120) converts the mmCIF template of the entry into a PDB file (that complies with the current PDB format version 2.1). After author consultation and review, the data are entered into the public archive for distribution. The entry in PDB format is forwarded to PDB for inclusion in the PDB archive. We welcome any comments or suggestions you may have on these procedures. The total holdings for the NDB as of December 1996 are 560 structures. ------------------- Recent Publications ------------------- H.M. Berman, D.L. Beveridge, S. Neidle, W.K. Olson, J. Westbrook, A. Gelbin, S.-H. Hsieh, L. Clowney, B. Schneider, and C. Zardecki, "The Nucleic Acid Database project" in Biological Structure and Dynamics, Proceedings of the Ninth Conversation of Biomolecular Stereodynamics (eds. R.H. Sarma and M.H. Sarma) Albany, NY: Adenine Press, 1-13 (1996). H.M. Berman, A. Gelbin, L. Clowney, S.-H. Hsieh, C. Zardecki, and J. Westbrook, "The Nucleic Acid Database: present and future", J. Res. Natl. Inst. Stand. Technol., 101, 243-257 (1996). ******************************************* 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 National Science Foundation and the Department of Energy // \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ //