NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 7. March 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 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 NDB AVAILABLE VIA GOPHER: ------------------------ All the information on the NDB file server are 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 NEW STRUCTURES: -------------- Since December, six new DNA structures have been added to the database. Five of these have coordinates available. In addition, new coordinates are available for seven DNA structures. The current release consists of updated tables describing the 216 DNA, RNA, and tRNA structures now contained in the database. Coordinates are available for 149 of these structures. The following new structures, with coordinates, have been added to the database: ADH038 5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3', SPERMINE N.Thota, X.H.Li, C.Bingman, M.Sundaralingam ADH039 5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3', SPERMIDINE N.Thota, X.H.Li, C.Bingman, M.Sundaralingam ADH041 5'-D(*GP*TP*CP*TP*AP*GP*AP*C)-3' A.Cervi, B.Langlois D'Estaintot, W.N.Hunter DDB033 5'-D(*CP*G)-3', PROFLAVIN, -2C B.Schneider, S.L.Ginell, H.M.Berman DDB034 5'-D(*CP*G)-3', PROFLAVINE, -130C B.Schneider, S.L.Ginell, H.M.Berman The bibliographic information for the following structure is available: ZDFA32 5'-D(*P(NC6)*CP*GP*(BR)CP*GP*CP*G*)-3' Y.-C.Jean, Y.-G.Gao, A.H.-J.Wang Coordinates for the following structures have been released: ADH012 5'-D(*CP*CP*CP*CP*GP*GP*GP*G)-3' T.E.Haran, Z.Shakked, A.H.-J.Wang, A.Rich ADH030 5'-D(*GP*GP*GP*TP*AP*CP*CP*C)-3', ROOM TEMPERATURE M.Eisenstein, F.Frolow, Z.Shakked, D.Rabinovich ADH031 5'-D(*GP*GP*GP*TP*AP*CP*CP*C)-3', 100K M.Eisenstein, F.Frolow, Z.Shakked, D.Rabinovich BDL041 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*IP*GP*CP*G)-3' G.A.Leonard, E.D.Booth, W.N.Hunter, T.Brown BDLB33 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(O)AP*GP*CP*G)-3' G.A.Leonard, A.Guy, T.Brown, R.Teoule, W.N.Hunter DDF036 5'-D(*TP*GP*AP*TP*CP*A)-3', 4'-EPIADRIAMYCIN B.Langlois D'Estaintot, B.Gallois, T.Brown, W.N.Hunter UDL018 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3' C.Kang, X.Zhang, R.Ratliff, R.Moyzis, A.Rich MOLECULAR GRAPHICS INCLUDING PACKING PICTURES NOW AVAILABLE: ----------------------------------------------------------- Our interface program to the relational database, "ndbquery", has been extended to produce several types of molecular graphics, including packing pictures. Molecular graphics are distributed as PostScript files. These files can be printed on a PostScript printer or viewed on a computer terminal using a PostScript viewer program. For best effect, use a color terminal. Several examples of these are available on the file server from the directory called molecular. Graphics for only one structure (BDJ025, 5'-D(*CP*GP*AP*TP*CP*GP*AP*TP*CP*G)-3', K.Grzeskowiak, K.Yanagi, G.G.Prive, R.E.Dickerson, J.Biol.Chem., V.266, 8861, 1991) are on the file server, but the same pictures are available upon request for any structure. The graphics examples can be obtained by sending the following mail message: To: nbdlib@helix.rutgers.edu Subject: send from molecular where the word is replaced by one of the file names as described below. The following files are available in the directory molecular. bdj025_one.ps This file contains a single view of the molecule. Each residue is colored differently for easy inspection on color terminals. bdj025_trip.ps This is a stereo triptych (A. R. Srinivasan and Wilma K. Olson. Viewing Stereo Drawings. J. Chem. Ed., V.66, 664, 1989) representation of the structure. A right handed molecule can be seen if the eyes are focused on the pair of pictures to the right or if a stereo device is focused on the pair to the left. bdj025_pack.ps This file contains four different views of the packing picture of the molecule. bdj025_packtrip.ps This is a stereo triptych representation of the packing picture of the molecule. A right handed molecule can be seen if the eyes are focused on the pair of pictures to the right or if a stereo device is focused on the pair to the left. bdj025_pack.coord This file contains the coordinate set for the packing picture of the molecule. To request similar graphics for any other structure, please send a mail message to the following address: To: ndbadmin@helix.rutgers.edu Please specify the NDB code and request the type of file. KINEMAGE FILES FOR A-DNAs: ------------------------- In addition to the previously released kinemage ( David C. Richardson and Jane S. Richardson. Protein Science, 1, 3-9, 1992) files of B-DNAs, the NDB file server now also contains kinemage files for all the A-DNAs. All of these are available from the directory called kinemages. 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@helix.rutgers.edu We will create the report, and mail it back via electronic mail. 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).