NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 5. October 1992. C------W C------W C--------W NNN NNN DDDDDD BBBBBBB C--------W C--------W NNNN NNN DDDDDDDD BBBBBBBBB C--------W C-------W NNNNN NNN DDD DDD BBB BBB C-------W C----W NNN NN NNN DDD DDD BBBBBBB C----W W NNN NNNNN DDD DDD BBB BBB W W--C NNN NNNN DDDDDDDD BBBBBBBBB W--C W-----C NNN NNN DDDDDD BBBBBBB W-----C W--------C W--------C W---------C W---------C W--------C W--------C W-----C THE NUCLEIC ACID DATABASE: W-----C C -------------------------- C C--W C--W C------W A RELATIONAL DATABASE OF NUCLEIC C------W C--------W ACID CRYSTAL STRUCTURES C--------W C--------W C--------W NDB, A RELATIONAL DATABASE: -------------------------- The Nucleic Acid Database (NDB) is a relational database, which is designed to facilitate the easy search for nucleic acid structures by any of the stored primary or derived structural features. Reports can then be created describing any properties of the selected structures. The reports available via the electronic mail server represent some examples of the kinds of tables that can be produced. Generally, each report includes a column for the NDB structure ID, and each row describes the selected features for the structure whose ID appears in the first column. Given the power of the relational database system, any set of structures can be selected, and any available information about them can be collected. The released reports give certain examples, but more specialized and sophisticated reports can be produced. GETTING STARTED WITH NDB: ------------------------ If you have never received a newsletter before, send the following e-mail message to receive complete access information. Please note that this message is read and replied to by a computer, so the subject line must be exactly as it appears here: To: ndblib@helix.rutgers.edu Subject: send access from newsletter To get personal help, send a message to this address: ndbadmin@helix.rutgers.edu NEW STRUCTURES: -------------- Since July, two new DNA structures have been added to the database. New coordinates are available for five DNA structures. The current release consists of updated tables describing the 204 DNA, RNA, and tRNA structures now contained in the database. Coordinates are available for 133 of these structures. The following new structures have been added to the database: DDF036 B.Langlois D'Estaintot, B.Gallois, T.Brown, W.N.Hunter 5'-D(*TP*GP*AP*TP*CP*A)-3', 4'-EPIADRIAMYCIN DDH037 S.Kamitori, F.Takusagawa 5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3', ACTINOMYCIN D Coordinates for the following structures have been released: AHJ040 M.Egli, N.Usman, S.Zhang, A.Rich 5'-D(*GP*GP*GP*TP*AP*TP*AP*CP*GP*C)-3'/ 5'-R(*GP*CP*GP*)-D(*TP*AP*TP*AP*CP*CP*C)-3' BDJ036 H.Yuan, J.Quintana, R.E.Dickerson 5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*CP*G)-3', CALCIUM BDJ037 H.Yuan, J.Quintana, R.E.Dickerson 5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*CP*G)-3', MAGNESIUM BDJ039 U.Heinemann, C.Alings, M.Bansal 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3' ZDFB31 B.Schneider, S.L.Ginell, R.Jones, B.Gaffney, H.M.Berman 5'-D(*CP*GP*UP*(NH2)AP*CP*G)-3' Please also note that the two coordinate sets originally present in file GDL001 (M.Coll, J.Aymami, G.A.Van Der Marel, J.H.Van Boom, A.Rich, A.H.-J.Wang, 5'-D(CP*GP*CP*GP*AP*TP*AP*TP*CP*GP*CP*G)-3', PDB file name: 1DNE) have been separated. Thus, now the entry GDL001 contains one coordinate set (conformation 1) and GDL004 the other (conformation 2). KINEMAGE FILES: -------------- The user-interface program to the Nucleic Acid Database is being extended to produce kinemage files (kinetic images) for the structures contained in NDB. Kinemages are described in the following article: David C. Richardson and Jane S. Richardson. 1992. The kinemage: A tool for scientific communication. Protein Science, 1, 3-9. Kinemage files for all structures will be available on the file server by the time of the next NDB newsletter. PERSONALIZED QUERIES: -------------------- Anyone who is interested in creating a report which is not found among the released ones, can receive a report request form by sending the following e-mail message: To: ndblib@helix.rutgers.edu Subject: send queries from newsletter (Note that this is the address of the automatic file server, so the Subject line must exactly look as it appears here for machine readability.) We will create the report, and mail it back via electronic mail. DIRECT ACCESS TO 'NDBQUERY': --------------------------- Our intention is to make the program "ndbquery" generally available to allow direct outside access to the database. In order to develop this, we need to select a few people to test the program by remotely logging in and making queries (as beta test users). Anyone interested in being considered for this testing process, should request an application form by sending the following e-mail message to the automatic file server: To: ndblib@helix.rutgers.edu Subject: send betatest from newsletter ACKNOWLEDGEMENTS: ---------------- The following article describing the Nucleic Acid Database project has appeared in the September issue of the Biophysical Journal: 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. From now on, researchers who make use of information obtained from NDB, should use this citation. The Nucleic Acid Database Project represents a collaborative effort between Helen Berman and Wilma Olson of Rutgers University and David Beveridge of Wesleyan University, and is funded by the Division of Instrumentation and Resources of the National Science Foundation (DIR 90 12772).