NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 14. March 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:80 FORMS BASED INTERFACE TO THE NDB ON WWW AVAILABLE: -------------------------------------------------- The Forms Query Interface is an easy and simple way of accessing the Nucleic Acid Database directly from our WWW server. Instructions and examples are provided with the template to aid the user's query. Structures may be selected by choosing the desired structure identifier, primary author, structure type, space group, and/or sequence. 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 query is then processed, and a Nucleic Acid Database Structure Query Results List is presented. 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); the full Atlas entry. NEW STRUCTURES: --------------- The current release consists of updated tables describing the 350 three-dimensional structures contained in the database. These include DNA, RNA, and tRNA structures, as well as protein/DNA complexes. Coordinates are available for 286 of these structures. The following new structures, with coordinates, have been added to the database: ADH056 M.Eisenstein, Z.Shakked 5'-D(*CP*CP*CP*CP*GP*GP*GP*G)-3' (TETRAGONAL, 288K) ADH057 M.Eisenstein, Z.Shakked 5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3'(TETRAGONAL, 115K, RE-REFINEMENT) ADH058 M.Eisenstein, Z.Shakked 5'-D(*GP*GP*CP*CP*GP*GP*CP*C)-3' (TETRAGONAL, 288K) ADH059 B.Langlois D'Estaintot, A.Dautant, C.Courseille, G.Precigoux 5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3', ORTHORHOMBIC AHJ060 C.Ban, B.Ramakrishnan, M.Sundaralingam 5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)-R(*G)-3' ARL037 S.R.Holbrook, C.Cheong, I.Tinoco Jr, S.-H.Kim 5'-R(*P*GP*GP*AP*CP*UP*UP*CP*GP*GP*UP*CP*C)-3' BDJ060 D.S.Goodsell, K.Grzeskowiak, R.E.Dickerson 5'-D(*CP*TP*CP*TP*CP*GP*AP*GP*AP*G)-3' BDJB57 L.A.Lipscomb, M.E.Peek, M.L.Morningstar, S.M.Verghis, E.M.Miller, A.Rich, J.M.Essigmann, L.D.Williams 5'-D(*CP*CP*AP*(O)GP*CP*GP*CP*TP*GP*G)-3' BDL059 K.Balendiran, S.T.Rao, C.Y.Sekharudu, G.Zon, M.Sundaralingam 5'-D(*CP*GP*CP*GP*TP*TP*AP*AP*CP*GP*CP*G)-3' DDF050 A.Dautant, B.Langlois D'Estaintot, B.Gallois, T.Brown, W.N.Hunter 5'-D(*CP*GP*AP*TP*CP*G)-3', IDARUBICIN AND SPERMINE GDHB25 X.Chen, B.Ramakrishnan, S.T.Rao, M.Sundaralingam 5'-D(*IP*CP*IP*CP*IP*CP*IP*C)-3', DISTAMYCIN GDJB29 M.L.Kopka, D.S.Goodsell, I.Baikalov, K.Grzeskowiak, D.Cascio, R.E.Dickerson 5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3', ANTHRAMYCIN 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 GDL030 K.Balendiran, S.T.Rao, C.Y.Sekharudu, G.Zon, M.Sundaralingam 5'-D(*CP*GP*CP*GP*TP*TP*AP*AP*CP*GP*CP*G)-3', NETROPSIN GDL032 C.M.Nunn, S.Neidle 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3', PROPAMIDINE GDLB31 D.S.Goodsell, M.L.Kopka, R.E.Dickerson 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(BR)CP*GP*CP*G)-3', NETROPSIN, RE-REFINEMENT 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' PDE004 L.S.Beese, V.Derbyshire, T.A.Steitz KLENOW FRAGMENT-DNA COMPLEX PDE013 K.Padmanabhan, K.P.Padmanabhan, J.D.Ferrara, J.E.Sadler, A.Tulinsky ALPHA-THROMBIN/D-PHE-PRO-ARG-CHLOROMETHYLKETONE-DNA COMPLEX PDE014 D.Kostrewa, F.K.Winkler ECO RV ENDONUCLEASE-DNA COMPLEX PDE015 D.Kostrewa, F.K.Winkler ECO RV ENDONUCLEASE-DNA COMPLEX PDE016 D.Kostrewa, F.K.Winkler ECO RV ENDONUCLEASE-DNA COMPLEX PDE017 X.Cheng, K.Balendiran, I.Schildkraut, J.E.Anderson PVUII ENDONUCLEASE-DNA COMPLEX PDR012 B.E.Raumann, M.A.Rould, C.O.Pabo, R.T.Sauer ARC REPRESSOR-OPERATOR COMPLEX PDR016 W.A.Lim, A..Hodel, R.T.Sauer, F.M.Richards LAMBDA REPRESSOR-OPERATOR COMPLEX PDT005 C.Wolberger, A.K.Vershon, B.Liu, A.D.Johnson, C.O.Pabo MAT-ALPHA2 HOMEODOMAIN-DNA COMPLEX PDT007 P.Koenig, T.J.Richmond GCN4-DNA COMPLEX PDT011 L.Fairall, J.W.R.Schwabe, L.Chapman, J.T.Finch, D.Rhodes TRAMTRACK DNA-BINDING DOMAIN (TTKDBD)-DNA COMPLEX PDT012 Y.Kim, J.H.Geiger, S.Hahn, P.B.Sigler TATA-BOX BINDING PROTEIN (YTBP)-DNA COMPLEX PDT016 P.C.M.Ma, M.A.Rould, H.Weintraub, C.O.Pabo MYOD BASIC-HELIX-LOOP-HELIX (BHLH)-DNA COMPLEX PDT017 R.Marmorstein, S.C.Harrison PPR1-DNA COMPLEX PDT019 J.D.Klemm, M.A.Rould, R.Aurora, W.Herr, C.O.Pabo OCT-1 POU DOMAIN-DNA COMPLEX PDV003 M.S.Chapman, M.G.Rossmann CANINE-PARVOVIRUS-DNA COMPLEX The coordinate sets of the following structures have been replaced: PDE001 J.Choi, Y.Kim, K.Chandrasekhar, P.A.Wilkosz, J.C.Grable, P.Greene, P.Hager, J.M.Rosenberg ECO RI ENDONUCLEASE-DNA COMPLEX PDV001 R.S.Hegde, S.R.Grossman, L.A.Laimins, P.B.Sigler BOVINE PAPILLOMAVIRUS-1 E2-DNA COMPLEX The bibliographic information for the following structures is available: PDR014 Z.Shakked, G.Guzikevich-Guerstein, F.Frolow, D.Rabinovich, A.Joachimiak, P.B.Sigler TRP REPRESSOR-OPERATOR-COMPLEX PDRC03 J.W.R.Schwabe, L.Chapman, J.T.Finch, D.Rhodes ESTROGEN RECEPTOR-DNA-COMPLEX PDT013 K.L.Clark, E.D.Halay, E.Lai, S.K.Burley HNF-3-DNA-COMPLEX PDT014 J.N.M.Glover, S.C.Harrison C-FOS-C-JUN-DNA-COMPLEX PDT015 G.Ghosh, G.Van Duyne, S.Ghosh, P.B.Sigler NF-KAPPA B P50 HOMODIMER-DNA COMPLEX PDT020 T.Ellenberger, D.Fass, M.Arnaud, S.C.Harrison E47-DNA-COMPLEX PRV002 C.Oubridge, N.Ito, P.R.Evans, C.-H.Teo, K.Nagal UIA SPLICEOSOMAL PROTEIN-RNA COMPLEX Coordinates are released only after authorization by the Brookhaven Protein Data Bank. COORDINATES OF PROTEIN/DNA COMPLEXES NOW AVAILABLE IN PDB FORMAT: ----------------------------------------------------------------- All the coordinates of protein/DNA complexes are now also available in PDB format, and are located in the directory coord_pdb. 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).