NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 9. September 1993. 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 NEW STRUCTURES: -------------- Since June, coordinates for 24 structures have been added to the database. In addition, the bibliographic information for two new structures has been made available. The current release consists of updated tables describing the 241 DNA, RNA, and tRNA structures now contained in the database. Coordinates are available for 190 of these structures. Note that coordinates are released only after the Brookhaven Protein Data Bank has given permission for release. The following new structures, with coordinates, have been added to the database: BDJ045 5'-D(*CP*CP*AP*AP*IP*AP*TP*TP*GP*G)-3' A.A.Lipanov, M.L.Kopka, M.Kaczor-Grzeskowiak, R.E.Dickerson BDJ051 5'-D(*CP*AP*TP*GP*GP*CP*CP*AP*TP*G)-3' D.S.Goodsell, M.L.Kopka, D.Cascio, R.E.Dickerson BDJB49 5'-D(*CP*CP*AP*GP*GP*CP*(M)CP*TP*GP*G)-3' M.Hahn, U.Heinemann BDJB50 5'-D(*CP*CP*AP*GP*GP*CP*(M)CP*TP*GP*G)-3' M.Hahn, U.Heinemann BDL042 5'-D(*CP*GP*TP*AP*GP*AP*TP*CP*TP*AP*CP*G)- 3' G.A.Leonard, W.N.Hunter BDL047 5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*AP*AP*CP*G)-3' A.D.DiGabriele, T.A.Steitz DDF041 5'-(*CP*GP*TP*AP*CP*G)-3',3'-DESAMINO-3'-(2-METHOXY-4- MORPHOLINYL)-DOXORUBICIN (FCE23672) M.Cirilli, F.Bachechi, G.Ughetto, F.P.Colonna, M.L.Capobianco ZDFS33 5'-ARA(*CP*)-D(*GP*)-ARA(*CP*)-D(*GP*)-ARA(*CP*)-D(*GP)-3' H.Zhang, G.A.Van Der Marel, J.H.Van Boom, A. H.-J.Wang Coordinates are now released for the following structures for which only bibliographic information had been available previously: ADH017 5'-D(*GP*GP*IP*GP*CP*TP*CP*C)-3' W.B.T.Cruse, J.Aymani, O.Kennard, T.Brown, A.G.C.Jack, G.A.Leonard ADH018 5'-D(*GP*GP*GP*GP*TP*CP*CP*C)-3' G.Kneale, T.Brown, O.Kennard, D.Rabinovich ADH019 5'-D(*GP*GP*GP*GP*CP*TP*CP*C)-3' W.N.Hunter, G.Kneale, T.Brown, D.Rabinovich, O.Kennard ADH020 5'-D(*CP*TP*CP*TP*AP*GP*AP*G)-3' W.N.Hunter, B.Langlois D'Estaintot, O.Kennard ADHB11 5'-D(*GP*GP*(BR)UP*AP*(BR)UP*AP*CP*C)-3' O.Kennard, W.B.T.Cruse, J.Nachman, T.Prange, Z.Shakked, D.Rabinovich AHJ015 5'-R(*GP*CP*GP*)-D(*TP*AP*TP*AP*CP*GP*C)-3' A.H.-J.Wang, S.Fujii, J.H.Van Boom, G.A.Van Der Marel, S.A.A.Van Boeckel, A.Rich BDFP24 5'-D(RP*GP(S)*CP*GP(S)*CP*GP(S)*C)-3' W.B.T.Cruse, S.A.Salisbury, T.Brown, R.Cosstick, F.Eckstein, O.Kennard BDL006 5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*AP*GP*CP*G)-3' H.C.M.Nelson, J.T.Finch, B.F.Luisi, A.Klug BDL009 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*TP*GP*CP*G)-3' W.N.Hunter, T.Brown, G.Kneale, N.N.Anand, D.Rabinovich, O.Kennard BDL010 5'-D(*CP*GP*CP*IP*AP*AP*TP*TP*AP*GP*CP*G)-3' P.W.R.Corfield, W.N.Hunter, T.Brown, P.Robinson, O.Kennard BDL011 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3' W.N.Hunter, T.Brown, O.Kennard BDL012 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*AP*GP*CP*G)-3' T.Brown, W.N.Hunter, G.Kneale, O.Kennard BDL014 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*GP*GP*CP*G)-3' T.Brown, G.A.Leonard, E.D.Booth, J.Chambers DDF018 5'-D(*CP*GP*AP*TP*CP*G)-3', DAUNOMYCIN M.H.Moore, W.N.Hunter, B.Langlois D'Estaintot, O.Kennard ZDFB14 5'-D(*(BR)UP*GP*CP*GP*CP*G)-3' T.Brown, G.Kneale, W.N.Hunter, O.Kennard ZDFB25 5'-D(*CP*GP*CP*GP*(M)CP*G)-3' L.Van Meervelt, M.H.Moore, P.K.T.Lin, D.M.Brown, O.Kennard The bibliographic information for the following structures is available: ADH042 5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3' B.Langlois D'Estaintot, A.Dautant, C.Courseille, G.Precigoux GDL022 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', HOECHST 33258 M.Sriram, G.A.Van Der Marel, H.L.P.F.Roelen, J.H.Van Boom, A.H.-J.Wang PERSONALIZED QUERIES: -------------------- Anyone who is interested in creating a report which is not found among the released ones can request a report by sending a message to the following e-mail address: To: ndbadmin@ndbserver.rutgers.edu We will create the report and send it back via electronic mail. NDB AVAILABLE VIA GOPHER: ------------------------ All the information on the NDB file server is now available via the Gopher service. The Internet Gopher is a distributed document delivery service which allows the user to access data from multiple hosts. The NDB gopher resides on host ndbgopher.rutgers.edu port 17105. So, on a character terminal based gopher, one would type the following command to connect to the NDB gopher server: gopher ndbgopher.rutgers.edu 17105 In addition, the NDB file server can also be accessed through the PDB Internet Gopher. 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 and Resources of the National Science Foundation (BIR 90 12772).