NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 15. July 1995. 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 using 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 selected 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@ndbserver.rutgers.edu Subject: send access from newsletter To get personal help, send a message to this address: ndbadmin@ndbserver.rutgers.edu SUMMARY OF NDB ACCESS INFORMATION: ---------------------------------- E-mail: To: ndblib@ndbserver.rutgers.edu Subject: send access from newsletter Anonymous ftp: ftp ndbserver.rutgers.edu Internet Gopher: gopher ndbgopher.rutgers.edu 70 World Wide Web: http://ndbserver.rutgers.edu NEW WWW INTERFACE TO THE NDB AVAILABLE: --------------------------------------- A new application interface to the NDB has been developed to help efficiently select structures from the NDB. Versions for the two WWW browsers, Netscape and Mosaic, are available. Structures may be selected by choosing the desired structure(s) based on a large variety of structural and experimental characteristics stored in the NDB. The structural features are stored in different tables and are grouped within the following categories: General information, structure description, refinement, crystallization, and data collection. (At this stage of development, it is advisable to use capital letters for all searches.) Operators, such as "equal to", "not equal to", "like", "like any", and "not like any" may be used to define a condition the attribute should meet. Several conditions may be joined together by using logical AND and OR operators. The Nucleic Acid Database Structure Query Results List is presented after executing the query. From this list, the user can select various output options: the coordinates in NDB or PDB format; the full NDB entry; the molecular structure using either a local viewer or a remote viewer (RasMol); or the full Atlas entry. NEW STRUCTURES: --------------- The current release consists of updated tables describing the 361 three-dimensional structures contained in the database. These include DNA, RNA, and tRNA structures, as well as protein/DNA (or RNA) complexes. Coordinates are available for 294 of these structures. The following new structures, with coordinates, have been added to the database: ARL062 H.Schindelin, M.Zhang, R.Bald, J.-P.Fuerste, V.A.Erdmann, U.Heinemann 5'-R(*UP*AP*AP*GP*GP*AP*GP*GP*UP*GP*AP*U)-3' GDL033 A.Czarny, D.W.Boykin, A.A.Wood, C.M.Nunn, S.Neidle, M.Zhao, W.D.Wilson 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', 5-(2-IMIDAZOLINYL)-2[2-(4-HYDROXYPHENYL)-5- BENZIMIDAZOLYL] BENZIMIDAZOLE GDLB24 Y.-G.Gao, M.Sriram, W.A.Denny, A.H.-J.Wang 5'-D(*CP*GP*CP*(E)GP*AP*AP*TP*TP*CP*GP*CP*G)-3', SN6999 PDE018 A.Jacobo-Molina, A.D.Clark Junior, R.L.Williams, R.G.Nanni, P.Clark, A.L.Ferris, S.H.Hughes, E.Arnold HIV-1 RT-DNA COMPLEX PTR002 J.J.Perona, M.A.Rould, T.A.Steitz GLUTAMINYL-TRNA SYNTHETASE-TRNA AND AMP COMPLEX (8 DEGREES C) PTR003 M.A.Rould, J.J.Perona, T.A.Steitz GLUTAMINYL-TRNA SYNTHETASE-TRNA AND AMP COMPLEX (-8 DEGREES C) UDG028 G.A.Leonard, S.Zhang, M.R.Peterson, S.J.Harrop, J.R.Helliwell, W.B.T.Cruse, B.Langlois D'Estaintot, O.Kennard, T.Brown, W.N.Hunter 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' The bibliographic information for the following structure is available: PDR018 W.Xu, M.A.Rould, S.Jun, C.Desplan, C.O.Pabo PAIRED DOMAIN-DNA COMPLEX UDI030 L.Van Meervelt, D.Vlieghe, A.Dautant, B.Gallois, G.Precigoux, O.Kennard 5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3' Coordinates are released only after authorization by the Brookhaven Protein Data Bank. ACKNOWLEDGEMENTS: ----------------- The following article describing the Nucleic Acid Database project appeared in the September, 1992 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. 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 anResources of the National Science Foundation (BIR 93 05135).