// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Volume 2. Number 1. January 1998. The NDB can be accessed through the BSR WWW site (http://ndbserver.rutgers.edu/) and its mirror sites (http://www.ebi.ac.uk/NDB/, http://ndbserver.nibh.go.jp/NDB/, http://ndb.sdsc.edu/). Comments, queries, and questions about NDB and this newsletter should be sent to ndbadmin@ndbserver.rutgers.edu. ---------------------------------------------------- Contents ---------------------------------------------------- The NDB announces the Biological Structure Resource: Structure Finder a la mode NDB mmCIF ---------------------------------------------------- The NDB announces the Biological Structure Resource --------------------------------------------------- The NDB Project has developed the Biological Structure Resource (BSR) site which includes: Structure Finder: Structure Finder provides access to a variety of macromolecular structure databases that have been developed by the NDB Project. a la mode: Databases for monomer units and ligands have been created by a la mode, which is A Ligand And Monomer Object Data Environment for building models. Nucleic Acid Database: The NDB assembles and distributes structural information about nucleic acids. mmCIF: mmCIF (macromolecular Crystallographic Information File) is the IUCr-approved data representation for macromolecular structures. The BSR is located at http://ndbserver.rutgers.edu/ and is mirrored at http://www.ebi.ac.uk/NDB/, http://ndbserver.nibh.go.jp/NDB/ and http://ndb.sdsc.edu/. Questions and comments about our new site and its organization are welcome! Please write to ndbadmin@ndbserver.rutgers.edu. ---------------- Structure Finder ---------------- Structure Finder provides access to a variety of macromolecular structure databases. The technology used to create these databases is the same as is used for the Nucleic Acid Database. The databases that can be accessed are: NDB: This curated database contains information about crystal structures that contain nucleic acids, including DNA, RNA, and protein-nucleic acid complexes. There are over 90 tables in the database with over 500 items that can be used to construct simple or complex queries. DNA-Binding Proteins: This curated database contains information about crystalline proteins that bind to DNA. Structures for proteins with and without DNA can be found here. NMR Nucleic Acids: This database contains information about nucleic acid containing structures that have been determined by NMR methods. Protein Plus: This database contains information about all of the structures found in the Protein Data Bank. These databases can be searched for specific structures, and then have reports generated about these structures by using the tools listed below. Please note that while the same tools are used for each database, the number of constraint options for searching and reporting are based upon level of curation in the database. More tables are available for the more highly curated databases. Search and Report Tools: ------------------------ Quick Search - offers a page of simple selection constraints for structure selection. Each Quick Search menu is tailored for the particular database. Items are entered or selected from a pop-up menu. After selecting "Execute Selection", the user is then presented with a results list containing the Structure ID and descriptor. Coordinates may be retrieved and RasMol may be used to view any of the structures in this list. Reports can be generated for the structures in this list using Quick Report. Quick Report - generates reports for the structures found using Quick Search. The user selects a report from the list provided and it is automatically generated. Different reports are available for each database. These reports can be printed and downloaded. Full Search - allows the user to search all of the tables found in the particular database. After selecting "Execute Selection", the user is then presented with a results list containing the Structure ID and descriptor. Coordinates may be retrieved and RasMol may be used to view any of the structures in this list. Reports can be generated for the structures in this list using Full Report. Full Report - generates reports for the structures found using Full Search. The user may select any combination of the tables found in the database to create reports. These reports can be printed and downloaded. Tutorials on using these tools are available from the Structure Finder main page and from each database main page. --------- a la mode --------- a la mode is an environment for building models of ligand and monomer molecular components. The information for building these models is gathered from the CSD and then put into mmCIF format. A database is then constructed which gives detailed information about the structure and chemistry of the derived models. At present, the database for the nucleotide monomer units is available. --------------------- Nucleic Acid Database --------------------- The NDB is organized in the following sections: Atlas. The NDB Atlas of nucleic acid containing structures highlights the special aspects of each structure in the NDB using a combination of text and graphics. Nucleic Acid structures are organized by structure type. Protein-nucleic acid structures are organized by function. Archives. The NDB Archives contain coordinate files, prepared reports, nucleic acid dictionaries, and other resources. New features include: *Prepared Reports organized by structure type. *The addition of chirally corrected coordinate files for nucleic acids and the processed coordinate files for protein-nucleic acid binding proteins. NDB Search. The NDB can be searched using the same tools as the other Structure Finder databases. NDB Search also provides: NDB Status Search - can be used to report the processing status of structures in the database. NDB Release Report - can be used to show which structures have been released since a user-specified date. Tutorials are available for all of these search tools at http://ndbserver.rutgers.edu/structure-finder/ndb/ and at all of the mirror sites. Deposition. Data for the crystal structures of nucleic acids should be deposited directly with the Nucleic Acid Database (NDB). A new shortened deposition form is available. General NDB contact information, NDB Newsletter subscription details, Information. and related WWW links are provided. mmCIF ----- The mmCIF WWW site is maintained at the BSR site. mmCIF (macromolecular Crystallographic Information File) is the IUCr-approved data representation for macromolecular structures. This site contains dictionaries, software tools, and more. Tutorials from the mmCIF Software Developers' Workshop can also be found at this site. ******************************************* 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, Joan Pontius, John Westbrook, and Christine Zardecki The Nucleic Acid Database Project is funded by the National Science Foundation and the Department of Energy // \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ //