NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 13. December 1994. 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 *************************************************************************** *************************************************************************** HAPPY HOLIDAYS TO ALL OF OUR NDB USERS! ** * * ** * ** * * ** ** * * ** *** *** *** ** * * ** * * * * * * ** * ** * * * * * * * * * * * * * * * * ***** * *** * * * *** * ***** * ** * * * ** * * * * * * * ** * * * ** **** * * ** ** * * **** * * * **** * * ** ** * * **** ** * * * ** * * * * ** * * * ** * ***** * * * * * * * * * ***** * * * *** * * * *** * * * * * * * * * * * * * * * * * * * ** * * ** ** * ** ** * * ** ** * * ** *** *** *** ** * * ** * *************************************************************************** *************************************************************************** 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: -------------- The current release consists of updated tables describing the 321 three-dimensional structures contained in the database. These include DNA, RNA, and tRNA structures, as well as protein/DNA complexes. Coordinates are available for 251 of these structures. The following new structures, with coordinates, have been added to the database: AHJS55 P.Lubini, W.Zuercher, M.Egli 5'-D(*GP*CP*GP*TP*)-(M)R(*AP*)-D(*TP*AP*CP*GP*C)-3' DDF049 C.K.Smith, G.J.Davies, E.J.Dodson, M.H.Moore 5'-D(*TP*GP*AP*TP*CP*A)-3', NOGALAMYCIN GDL027 C.M.Nunn, T.C.Jenkins, S.Neidle 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', GAMMA-OXAPENTAMIDINE PDE009 J.-A.Feng, R.C.Johnson, R.E.Dickerson HIN RECOMBINASE-DNA COMPLEX PDE010 A.M.Buckle, A.R.Fersht BARNASE-DNA COMPLEX PDE011 H.Pelletier, M.R.Sawaya, A.Kumar, S.H.Wilson, J.Kraut RAT DNA POLYMERASE BETA-DNA-2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE (DDCTP) COMPLEX (SPACE GROUP P 61) PDE012 H.Pelletier, M.R.Sawaya, A.Kumar, S.H.Wilson, J.Kraut RAT DNA POLYMERASE BETA-DNA-2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE (DDCTP) COMPLEX (SPACE GROUP P 21) PDR015 D.W.Rodgers, S.C.Harrison 434 REPRESSOR-OPERATOR COMPLEX UDD023 C.Kang, I.Berger, C.Lockshin, R.Ratliff, R.Moyzis, A.Rich 5'-D(*CP*CP*CP*T)-3' URB020 E.Shefter, M.Barlow, R.A.Sparks, K.N.Trueblood 5'-R(*AP*U)-2' ZDF040 M.Doi, M.Inoue, K.Tomoo, T.Ishida, Y.Ueda, M.Akagi, H.Urata 5'-D(*CP*GP*CP*GP*CP*G)-3' The bibliographic information for the following structures is available: ADH059 B.Langlois D'Estaintot, A.Dautant, C.Courseille, G.Precigoux 5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3', ORTHORHOMBIC BDJ061 Z.Shakked, G.Guzikevich-Guerstein, F.Frolow, D.Rabbinovich, A.Joachimiak, P.B.Sigler 5'-D(*CP*CP*AP*CP*TP*AP*GP*TP*GP*G)-3' GDHB25 X.Chen, B.Ramakrishnan, S.T.Rao, M.Sundaralingam 5'-D(*IP*CP*IP*CP*IP*CP*IP*C)-3', DISTAMYCIN GDL026 M.C.Vega, I.Garcia-Saez, J.Aymami, R.Eritja, G.A.Van Der Marel, J.H.Van Boom, A.Rich, M.Coll 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3', HOECHST 33258 GDL028 N.Spink, D.G.Brown, J.V.Skelly, S.Neidle 5'-(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3', HOECHST 33258 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 PDT011 L.Fairall, J.W.R.Schwabe, L.Chapman, J.Finch, D.Rhodes TRAMTRACK DNA-BINDING DOMAIN (TTKDBD)-DNA COMPLEX UDD024 L.Chen, L.Cai, X.Zhang, A.Rich 5'-D(*CP*CP*CP*C)-3' UDF025 L.Malinina, L.Urpi, X.Salas, T.Huynh-Dinh, J.A.Subirana 5'-D(*CP*CP*GP*CP*GP*G)-3' Coordinates for the following structures have been released: ADH054 S.Kamitori, F.Takusagawa 5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3' AHIB53 W.Cruse, P.Saludjian, E.Biala, P.Strazewski, T.Prange, O.Kennard 5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BR)U)-3' ADH010 Z.Shakked, D.Rabinovich, O.Kennard, W.B.T.Cruse, S.A.Salisbury, M.A.Viswamitra 5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3' BDJ055 D.S.Goodsell, M.Kaczor-Grzeskowiak, R.E.Dickerson 5'-D(*CP*CP*AP*TP*TP*AP*AP*TP*GP*G)-3' BDLB54 G.A.Leonard, K.E.McAuley-Hecht, N.J.Gibson, T.Brown, W.P.Watson, W.N.Hunter 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(ETH)AP*GP*CP*G)-3' DDDB46 M.E.Peek, L.A.Lipscomb, J.A.Bertrand, Q.Gao, B.P.Roques, C.Garbay-Jaureguiberry, L.D.Williams 5'-D(*(BR)CP*GP*CP*G)-3', FLEXI-DI DDH048 S.Kamitori, F.Takusagawa 5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3', ACTINOMYCIN D PDR013 C.L.Lawson, J.Carey TRP REPRESSOR/OPERATOR HALF-SITE COMPLEX Coordinates are released only after authorization by the Brookhaven Protein Data Bank. New parameters available for XPLOR: ----------------------------------- The NDB Project has developed a new set of parameters, and a corresponding topology file, for refinement of nucleic acid-containing structures using XPLOR. These new parameters have been used successfully in the refinement of both B-DNA and B-DNA/protein complexes. Currently the sugar parameters are those for deoxy sugars with the C2'-endo conformation. Values for riboses and sugars with the C3'-endo conformation will be added shortly. The new parameter file and topology file are available electronically on the World Wide Web under the following URL: http://ndbserver.rutgers.edu:80 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 also available via Gopher: ----------------------------- All the information on the NDB file server is also 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 70. On a character terminal based gopher, one would type the following command to connect to the NDB gopher server: gopher ndbgopher.rutgers.edu 70 In addition, the NDB file server can also be accessed through the PDB Internet Gopher. On a terminal running X windows, one could type xgopher to run the X version of 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).