// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Number 22. July 1997. The NDB can be accessed through our WWW site (http://ndbserver.rutgers.edu) and its mirror sites (http://www.ebi.ac.uk/NDB/ and http://ndbserver.nibh.go.jp/NDB/). Comments, queries, and questions about NDB and this newsletter should be sent to ndbadmin@ndbserver.rutgers.edu. -------------------------------- Contents -------------------------------- ACA St. Louis Area Code Change Chirality Checks Summer Projects Meetings Structures in the NDB NDB Family -------------------------------- ACA St. Louis ------------- We look forward to seeing those of you who will be attending the American Crystallographic Association Annual Meeting this summer. Helen Berman has co-organized the ACA Transactions Symposium with Gary Gilliland to be held on Monday, July 21. The topic is "Structural Informatics." John Westbrook will co-chair a CIF Workshop with Herbert Bernstein. It will be held on Tuesday, July 22. The NDB group will also present three posters: P189 - L. Clowney, J. Westbrook and H. M. Berman LIGANDDB - Building a database of high resolution crystallographic models for common macromolecular ligands. P190 - Z. Feng, A. Gelbin, J. Westbrook and H. M. Berman Protein Finder - A relational database of protein structures and supporting tools. P191 - A. Gelbin, Z. Feng, J. Westbrook and H. M. Berman The versatile query interface to the Nucleic Acid Database (NDB). The NDB will also be demonstrating our software at the Silicon Graphics booth. Please stop by and say hello! Area Code Change ---------------- Our area code has been changed from 908 to 732. Our contact information is: The Nucleic Acid Database Department of Chemistry Rutgers University Piscataway, NJ 08855-0939 phone: 732 445 0103 fax: 732 445 4320 email: ndbadmin@ndbserver.rutgers.edu Chirality Checks ---------------- Many of you may have seen the recent article "Chirality errors in nucleic acid structures" by P. Schultze & J. Feigon (Nature (1997) 387, p. 668). Starting July 1, we will include chirality checks as part of our structure validation procedure for all structures deposited at NDB, and will report the results to the depositors. In reviewing all of the nucleic acid structures currently in the database, we have confirmed that the nomenclature for the phosphate oxygen atoms, O1P and O2P, are often reversed. (The standard IUBMB nomenclature is defined according to C. Liebecq. Compendium of Biochemical Nomenclature and Related Documents, 2nd ed. Portland Press: London and Chapel Hill, 1992, page 121.) We will report the relabeling of the phosphate oxygen atoms to the depositors. Summer Projects: NDB 1997 Research Experience ---------------------------- Our undergraduate research projects are well on their way. Students are working on adding new data items to the protein-nucleic acid structures, developing a ligand database, creating correspondences between the NDB and the Biological Macromolecule Crystallization Database (BMCD) at CARB, and creating more output options for our WWW Interface. Our first result is that the students are now able to speak CIF at a high level! We are all very excited by the quality and enthusiasm that is being put into these projects. Be sure to check back with us in the fall for more information on these ventures. Past summer projects have included the NDB Pictorial and Musical Atlases, and mmCIF software programs. Meetings -------- Congress of Molecular Medicine, Berlin, Germany May 3-5 Anke Gelbin presented the poster "The Nucleic Acid Database: a research tool for the study of nucleic acid structures" at the Congress of Molecular Medicine sponsored by the Max-Delbruck-Center for Molecular Medicine. 10th Conversation in Biomolecular Stereodynamics, Albany, NY June 17-21 Helen Berman recently attended the 10th Conversation in Biomolecular Stereodynamics in Albany, NY for the NDB and presented a talk entitled "Effects of crystal packing and protein interactions on DNA structure" by Helen M. Berman, Samuel Engel, Michael Mehnert and John Westbrook. This talk was the result of undergraduate research which began as one of last summer's student research projects. Wilma Olson and Xiangjun Lu presented a poster entitled "Working towards an optimized library of routines for the analysis and reconstruction of nucleic acid structure." DNA Topology II, DIMACS, Rutgers University, Piscataway, NJ April 3-4 Targeting Nucleic Acids, Rutgers University, Piscataway, NJ June 1-3 A poster "The Nucleic Acid Database (NDB)" was presented at the DNA Topology II conference sponsored by Discrete Mathematics and Theoretical Computer Science (DIMACS), the National Program in Mathematics and Molecular Biology based at Florida State University (PMMB) and the Center for Molecular Biophysics and Biophysical Chemistry (CMBBC) at Rutgers University. The NDB also presented a poster entitled "The Nucleic Acid Database: a research tool for the study of nucleic acid structures" at the Targeting Nucleic Acids Symposium sponsored by the CMBBC at Rutgers University. Structures in the NDB --------------------- ----------------------------------- DNA 369 DNA/RNA Hybrids 18 PNA 2 Protein-NA Complexes 210 RNA 58 ----------------------------------- NDB Family ----------- The NDB welcomes Alison Feng to the world! Alison was born, weighing 7 lbs. 8 oz., on May 14 to Xuelian Liang and Zukang Feng. ******************************************* 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 // \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ //