// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Number 19. September 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/). *** CONTENTS Atlas of Nucleic Acid Structures Musical Atlas XVII IUCr Congress and General Assembly mmCIF Software Tools NDB Summer Program NDB Holdings Electronic Library Update Deposition Information *** -------------------------------- Atlas of Nucleic Acid Structures -------------------------------- The WWW Atlas of Nucleic Acid Structures has been completely updated to include entries for all of the structures in the database with coordinates. Each entry highlights the structural information for a particular molecule, provides three-dimensional graphic images of the structure, and in most cases, presents a picture of the crystal packing. These Atlas pages, including the graphics, have been created using the Atlas Report Option of NDBQUERY. For some molecules, custom figures have been drawn using either NDBVIEW (Macskassay, 1991) or INSIGHT (Biosym Technologies, San Diego) to highlight their structural features. This Atlas is available at http://ndbserver.rutgers.edu/NDBATLAS/index.html. ------------- Musical Atlas ------------- A Musical Atlas has been created for selected B-DNA structures. Aural representations of the DNA sequences have been composed to provide another perspective on these structures. For a more detailed explanation of this project, please look at "About this Atlas" at http://ndbserver.rutgers.edu/MusicAtlas/index.html. Please note that you will need hardware and software that allows you to listen to .AU and .WAV files to hear these compositions. This project will be continued so that hopefully all nucleic acid sequences can find their voices! -------------------------------------------------- XVII IUCr Congress and General Assembly in Seattle -------------------------------------------------- Several members of the NDB group attended the IUCr Congress and General Assembly in August. We enjoyed seeing many of you at the poster session and at the computer demonstrations. Your questions and suggestions will help us to improve the NDB. ------------------------ mmCIF Software and Tools ------------------------ A full suite of tools has been developed for use with the new mmCIF dictionary. Documentation and source programs can be found at http://ndbserver.rutgers.edu/mmcif-interface/. These were presented at the CIF Workshop in Seattle and at the Computer School that followed. Of particular utility is the mmCIF Input Tool, which is a simple WWW forms- based interface that was developed to aid the preparation of a mmCIF data file. It is possible to start from scratch, from an already existing mmCIF data file, or from a file in PDB format. The user selects the category group and category to fill in the desired data items. The mmCIF Input Tool provides help wherever it is needed by conveniently linking to the definitions and examples contained in the mmCIF dictionary. In the near future, we will make this tool available for easy data deposition. A subset of the complex mmCIF dictionary will then be used for this reason. ------------------ NDB Summer Program ------------------ The NDB organized a summer program for undergraduate and high school students at Rutgers University. A total of eleven students learned how to work with the NDB programs, create molecular graphics, create cross references with other databases and write CIF code. The students updated the full Atlas, composed the music for the Musical Atlas, created new CIF tools, and participated in a number of other NDB related research projects. The funding for the student participants came from a variety of sources, including the NSF, NIST, and HHMI. We enjoyed having the students in the lab this summer and are pleased that many have returned to work on new Independent Study Projects this semester. ------------ NDB Holdings ------------ 461 Structures as of September 6, 1996 -------------------------------------- 59 A-DNA 15 A-RNA 83 B-DNA 19 RNA-Drug complexes 52 Z-DNA 10 tRNA 106 DNA-Drug complexes 2 Ribozymes 11 Single stranded DNA 12 Single stranded RNA 3 Parallel stranded DNA 1 Parallel stranded RNA 7 Quadruplexes 15 DNA/RNA Structures 68 Protein-DNA Complexes 8 Protein-RNA Complexes ------------------------- Electronic Library Update ------------------------- As always, coordinate files are available via electronic mail. Due to changes in our operating system, the process for retrieving files has changed. To retrieve coordinate files, mail should be sent to ndblib@ndbserver.rutgers.edu containing ftp commands in the body of the message. To retrieve the PDB coordinate files for addb01, for example, the following message should be sent: To: ndblib@ndbserver.rutgers.edu Subject: **text follows this line** open cd pub/coord_pdb get addb01.pdb quit You will first receive a message telling you that your request is being processed. This will be followed by the coordinate file a few minutes later. For more information, send the message "help" to ndblib@ndbserver.rutgers.edu. ---------- DEPOSITION ---------- As of January 1, 1996, NDB has been the direct deposition site for crystal structures of oligonucleotides. When depositing structures, the following components are needed: *Coordinates Coordinates should be submitted by electronic mail to deposit@ndbserver.rutgers.edu. PDB or mmCIF are the preferred file formats for deposition. *Deposition form At present, the PDB deposition form may be used. The full version and a shortened version of the deposition form appropriate for nucleic acid data submission is available at the NDB WWW site and at the ftp site: anonymous ftp: ftp ndbserver.rutgers.edu >cd pub >get dep_form.v95 (full PDB version) or >get dep_form.ndb (shortened version for Nucleic Acids) *Manuscript The paper (p)reprint should be sent via facsimile or air mail to the NDB at the address below. Its content is essential for structure checking. *Structure factors Structure factors may be submitted in any format. We strongly encourage you to submit these data. *Addresses for deposition* Electronic mail: deposit@ndbserver.rutgers.edu Air mail: Dr. Anke Gelbin The Nucleic Acid Database Department of Chemistry Rutgers, The State University of New Jersey Wright-Rieman Laboratories Piscataway, NJ 08855-0939 USA Fax: 908-445-4320 *Deposition Procedures* *NDB structure ID code An NDB ID code will be assigned after all three required components of the deposition (coordinates, deposition form, and preprint) have been submitted. *Author's Approval The author will receive the processed file in PDB format to review and give permission for release. *Archiving The structure will be placed in the NDB as soon as the author gives permission for release. The file will be sent to PDB for inclusion in the PDB archive. ************************************** 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 and the Department of Energy // \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ //