NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 8. June 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 March, 15 new DNA structures have been added to the database. 14 of these have coordinates available. In addition, new coordinates are available for three DNA structures. The current release consists of updated tables describing the 231 DNA, RNA, and tRNA structures now contained in the database. Coordinates are available for 166 of these structures. The following new structures, with coordinates, have been added to the database: ADL045 5'-(*CP*CP*GP*TP*AP*CP*GP*TP*AP*CP*GP*G)-3' C.A.Bingman, G.Zon, M.Sundaralingam ADL046 5'-(*GP*CP*GP*TP*AP*CP*GP*TP*AP*CP*GP*C)-3' C.Bingman, S.Jain, G.Zon, M.Sundaralingam AHJ043 5'-R(*GP*)-D(*CP*GP*TP*AP*TP*AP*CP*GP*C)-3' M.Egli, N.Usman, A.Rich AHJ044 5'-D(*GP*CP*GP*TP*)-R(*AP*)-D(*TP*AP*CP*GP*C)-3' M.Egli, N.Usman, A.Rich BDJ043 5'-D(*CP*CP*AP*AP*CP*IP*TP*TP*GP*G)-3', TRIGONAL A.Lipanov, M.L.Kopka, M.Kaczor-Grzeskowiak, J.Quintana, R.E.Dickerson BDJ044 5'-D(*CP*CP*AP*AP*CP*IP*TP*TP*GP*G)-3', MONOCLINIC A.Lipanov, M.L.Kopka, M.Kaczor-Grzeskowiak, J.Quintana, R.E.Dickerson BDJB48 5'-D(*CP*GP*AP*TP*CP*GP*(M)AP*TP*CP*G)-3' I.Baikalov, K.Grzeskowiak, K.Yanagi, J.Quintana, R.E.Dickerson BDL046 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*GP*GP*CP*G)-3' J.V.Skelly, K.J.Edwards, T.C.Jenkins, S.Neidle DDF038 5'-D(*TP*GP*AP*TP*CP*A)-3', IDARUBICIN B.Gallois, B.Langlois D'Estaintot DDF039 5'-D(*CP*GP*GP*CP*CP*G)-3', DAUNOMYCIN G.A.Leonard, T.W.Hambley, K.Mcauley-Hect, T.Brown, W.N.Hunter DDF040 5'-D(*TP*GP*GP*CP*CP*A)-3', ADRIAMYCIN G.A.Leonard, T.W.Hambley, K.Mcauley-Hect, T.Brown, W.N.Hunter GDL018 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', NETROPSIN M.Sriram, G.A.van der Marel, H.L.P.F.Roelen, J.H.van Boom, A.H.-J.Wang GDLB17 5'-D(*CP*GP*CP*(E)GP*AP*AP*TP*TP*CP*GP*CP*G)-3', NETROPSIN M.Sriram, G.A.van der Marel, H.L.P.F.Roelen, J.H.van Boom, A.H.-J.Wang UDBP19 5'-D(*AP(M)*T)-3' K.K.Chacko, K.Lindner, W.Saenger, P.S.Miller The bibliographic information for the following structure is available: ADH047 5'-(*GP*TP*GP*CP*GP*CP*AP*C)-3' C.Bingman, X.Li, G.Zon, M.Sundaralingam Coordinates for the following structures have been released: BDL040 5'-D(*CP*GP*CP*IP*AP*AP*TP*TP*CP*GP*CP*G)-3' J.C.Xuan, I.T.Weber DDF035 5'-D(*TP*GP*TP*AP*CP*A)-3', 4'-EPIADRIAMYCIN G.A.Leonard, T.Brown, W.N.Hunter ZDH030 5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3' V.D.Kumar, R.W.Harrison, L.C.Andrews, I.T.Weber EXTENDED GRAPH OPTIONS NOW AVAILABLE: ------------------------------------ In addition to the molecular graphics announced earlier (see newsletter of March 1993), scatter charts, line charts, column charts, and pie charts are now also available through the server. Our interface program to the relational database, "ndbquery", can produce different types of graphs depicting the relationships among several structural properties of any groups of structures. These graphs are distributed as PostScript files, which can be printed on a PostScript printer or viewed on a computer terminal using a PostScript viewer program. For best results, use a color terminal. The plot chart examples can be obtained by sending the following mail message: To: nbdlib@ndbserver.rutgers.edu Subject: send from plots where the word is replaced by one of the file names as described below. The following files are available in the directory 'plots': torsion_scatter.ps This file contains four scatter charts on a page, illustrating the statistical correlation of four torsion angles with the torsion angle Alpha (O3'-P-O5'-C5') in B-DNA. epsilon_chi.ps This file contains a scatter chart and a line chart on a page. The scatter chart illustrates the correlation between torsion angles epsilon (C4'-C3'-O3'-P) and chi (O4'-C1'-N1-C2) in B-DNA. The line chart below it shows the distribution of the torsion angle epsilon for each different residue type in B-DNA. types_pie.ps This file contains a pie chart visualizing the distribution of A-, B-, Z-, unusual, and right-handed drug complexed DNAs available in the Nucleic Acid Database. year_col.ps This file contains a column chart showing the number of newly solved structures described in the literature each year between 1972 and 1993. To request similar graphics, please send a mail message to the following address: To: ndbadmin@ndbserver.rutgers.edu To obtain more information about the molecular graphics available, please refer to our March 1993 newsletter, or send the following request: To: nbdlib@ndbserver.rutgers.edu Subject: send index from molecular 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).