// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Volume 2. Number 3. October 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. ********************************************************************* Special Announcement: Rutgers, UC San Diego, and NIST win grant to manage Protein Data Bank ********************************************************************* We are pleased to announce that the Research Collaboratory for Structural Bioinformatics (RCSB), a consortium composed of Rutgers, the State University of New Jersey; the University of California at San Diego; and the National Institute of Standards and Technology (NIST), has received a five-year award from the National Science Foundation (NSF), the Department of Energy (DOE), and two units of the National Institutes of Health: the National Institute of General Medical Sciences (NIGMS) and the National Library of Medicine (NLM) to operate and significantly extend the capabilities of the Protein Data Bank (PDB). The NDB, a charter member of the RCSB, as part of this project will extend the services that the NDB has provided for nucleic acids to all macromolecules. Many new services and capabilities will be added to the RCSB site throughout the year. NDB users will benefit by having access to more methods for macromolecular comparison and analysis. Currently maintained by Brookhaven National Laboratory, the PDB's change in management will be transparent and seamless as it moves to the RCSB with the addition of new capabilities for searching and for improving the consistency and content of existing and future depositions. The official announcement, FAQ, and grant proposal are available at http://www.rcsb.org/. What is the RCSB? ----------------- The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium dedicated to improving our understanding of the function of biological systems through an understanding of 3-D biological macromolecular structure. RCSB integrates a variety of production-level data and software resources and shares research results and software. The principal members of the RCSB are: Helen M. Berman, the director of the project, is a Professor in the Department of Chemistry and a member of the Waksman Institute at Rutgers, the State University of New Jersey. Dr. Berman founded and is currently the director of the Nucleic Acid Database Project. John Westbrook, a Project Team Leader, is a Research Associate Professor in the Department of Chemistry at Rutgers, the State University of New Jersey. Dr. Westbrook is the principal architect of the Nucleic Acid Database and is the author of the Dictionary Definition Language used by mmCIF. Peter Arzberger, a Project Team Leader, is the Executive Director of the National Partnership for Advanced Computational Infrastructure (NPACI) which is led by UC San Diego. Phil Bourne, a Project Team Leader, is a Senior Staff Scientist at the San Diego Supercomputer Center and an Adjunct Professor in the Department of Pharmacology, UCSD and the Burnham Institute. Dr. Bourne has developed several databases, including WPDB, MOOSE, and Structure Neighbors. Gary Gilliland, a Project Team Leader, is the Chief of the Biotechnology Division of the Chemical Science and Technology Laboratory of NIST and an adjunct Professor of the University of Maryland Biotechnology Institute at the Center for Advanced Research in Biotechnology (CARB). Dr. Gilliland founded the Biological Macromolecular Crystallization Database (BMCD). Phoebe Fagan, a Project Team Leader, is a program manager in the Standard Reference Data Program at NIST. Previously, Ms. Fagan headed the database development group within NIST Standard Reference Data Program and initiated its archive. What will the transition process be like for PDB and NDB users? --------------------------------------------------------------- The RCSB is committed to a smooth and seamless transition. At the beginning of the transition period, all procedures will remain the same. Over time, new facilities and functions will be added to make the submission and retrieval of data simpler. * Deposition NDB: Crystal structures of oligonucleotides should continue to be submitted directly to the Nucleic Acid Database (deposit@ndbserver.rutgers.edu). PDB: Data for protein structures should continue to be deposited using the current system of either AutoDep or the PDB Deposition Form, which are available at http://www.pdb.bnl.gov/ and http://www2.ebi.ac.uk/pdb/. RCSB: During the transition period, new tools to simplify the deposition process will be made available at the RCSB Web site (http://www.rcsb.org/). * Query NDB: The NDB will continue to maintain and develop the database and search and report interfaces available from Structure Finder (http://ndbserver.rutgers.edu/NDB/structure-finder/). PDB: The current search tools from the PDB (3DB Browser and PDB Lite) will continue to be available from the PDB WWW sites. RCSB: The RCSB has created a query interface that will become available at http://www.rcsb.org/. This integrated query interface examines all structures contained in the PDB and NDB by passing interactive queries to one or more of the following databases: NDB, Proteins Plus, BMCD, MOOSE, PDBObs, and Structure Neighbors. Queries can be iterative -- the output of one query can be used as input to the next query and across multiple structures (i.e., all members of a specific protein family). * Access NDB: Access to the NDB will continue to be available from the NDB WWW sites. PDB: All of the PDB options that were available through Brookhaven's PDB will continue to be available, including the Web sites, e-mail, ftp, and CD-ROM. All tools and files will remain in their current locations and directory trees. RCSB: Over the course of the next year, the RCSB will release new tools at the RCSB site at http://www.rcsb.org/. * Current Archives A project is underway to revisit all existing structures to provide more complete and consistent annotation and to remove any inconsistencies of a historic nature. This project will use the same software that is used to process structures at the NDB. So far, approximately 2,000 of the existing 8,000 structures have been reviewed. NDB Services ------------ The NDB Project will continue to provide the multitude of high-quality structural biological resources that our users have come to expect. Our future plans include the release of NUCheck (Feng, Westbrook, and Berman, 1998), a program that generates validation reports for nucleic acids. ******************************************* 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 Zukang Feng, Shri Jain, Bohdan Schneider, John Westbrook, and Christine Zardecki The Nucleic Acid Database Project is funded by the National Science Foundation and the Department of Energy // \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ //