// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Number 23. October 1997. The NDB can be accessed through our WWW site (http://ndbserver.rutgers.edu) and its mirror sites (http://www.ebi.ac.uk/NDB/, http://ndbserver.nibh.go.jp/NDB/ and http://ndb.sdsc.edu/). Comments, queries, and questions about NDB and this newsletter should be sent to ndbadmin@ndbserver.rutgers.edu. ----------------------------------------------- Contents ----------------------------------------------- New NDB Mirror: San Diego Supercomputer Center NDB Atlas: Protein Functions mmCIF Software Developers' Workshop mmCIF Coordinate Files: New Data Items NDB Archives: NMR Structures Structures in the NDB ----------------------------------------------- New NDB Mirror: San Diego Supercomputer Center ----------------------------------------------- We are pleased to announce that the NDB is now mirrored at the San Diego Supercomputer Center (SDSC) in San Diego, California at http://ndb.sdsc.edu/. Our liason at the SDSC is Professor Philip Bourne. This site is updated regularly, as are our mirrors at the EBI (http://ndbserver.ebi.ac.uk/NDB/) and at AIST-NIBH (http://ndbserver.nibh.go.jp/NDB/). NDB Atlas: Protein Functions ----------------------------- The Protein/Nucleic Acid Complexes section of the NDB Atlas of Nucleic Acid Structures is now organized by function. Protein/DNA Complexes are categorized as Enzymes, Regulatory, Structural, Peptide Nucleic Acid-DNA Complexes, or Other. Protein/RNA Complexes are arranged as Enzymes, Regulatory, or Structural. Additionally, there are now images available for all structures with released coordinates. This latest release of the Atlas reflects the work of the students who curated DNA-binding proteins as part of the NDB Summer Research Experience. mmCIF Software Developers' Workshop ----------------------------------- The mmCIF Software Developers' Workshop was held at Rutgers University on October 17-19, 1997. Thirty-five participants representing laboratories in Europe, Australia, and the United States gathered to discuss how best to implement the newly approved data representation for macromolecular structures called mmCIF. The workshop addressed topics including adapting existing applications to mmCIF, creating new applications to exploit the capabilities of DDL2 and mmCIF, use of existing mmCIF software tools and packages, and detailed presentations on the content of the DDL2 and mmCIF dictionaries. Discussion also focused on the requirements for new mmCIF software and dictionary content, and on the coordination of these ongoing development activities. There was a mix of tutorial, hands-on, and discussion sessions. This workshop was organized by Helen M. Berman, Paula Fitzgerald, and John Westbrook, sponsored by the Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), and co-funded by the Rutgers University Bioinformatics Initiative, the National Science Foundation (NSF), and the International Union of Crystallography (IUCr). Silicon Graphics provided the computers used in the workshop. mmCIF Software Tutorials and other information about the conference is available at http://ndbserver.rutgers.edu/workshop/. NDB Archives: NMR Structures ----------------------------- Using Protein Finder, the NDB has searched for nucleic acid-containing structures determined by NMR and has placed the coordinates for the resulting files on our ftp server. The index page lists each structure by the PDB ID, first author, and compound name. Modified bases are designated by a "+". These structures can be accessed from the NDB ftp server (ndbserver.rutgers.edu) in the directory /pub/na-nmr-coord or from the Archives section of NDB WWW site and its mirrors. If you have any questions or comments, please let us know at ndbadmin@ndbserver.rutgers.edu. mmCIF Coordinate Files: New Data Items --------------------------------------- The mmCIF data files currently available on our server are now populated with more data items. Previously, the mmCIF data files contained only coordinate, unit cell, and bibliographic data items. The files have now been populated with additional data items which describe components of chemical structure, the computational details of the experiment, the diffraction experiment, chemical entities, details of the experimental conditions, details about the Protein Data Bank's file format and processing codes, refinement information, and the details of reflection measurements. These files are available from the NDB WWW Interface, the Archives section of the WWW site, and from our ftp server at ndbserver.rutgers.edu in the directory /pub/cif-coord. Information about these category groups is available from the mmCIF dictionary section of our mmCIF site at http://ndbserver.rutgers.edu/NDB/mmcif/dictionary/. Structures in the NDB --------------------- ----------------------------------- DNA 374 DNA/RNA Hybrids 18 Peptide-NA Complexes 2 Protein-NA Complexes 219 RNA 63 ----------------------------------- ******************************************* 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, John Westbrook, and Christine Zardecki The Nucleic Acid Database Project is funded by the National Science Foundation and the Department of Energy // \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ //