NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 4. July 1992. 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 INTRODUCTION: ------------ Since April, nine new DNA structures have been added to the database. New coordinates are available for four DNA structures. The current release consists of updated tables describing the 201 DNA, RNA, and tRNA structures now contained in the database. Coordinates are available for 127 of these structures. LIST OF NEW STRUCTURES: ---------------------- The following new structures have been added to the database: AHJ040 M.Egli, N.Usman, S.Zhang, A.Rich 5'-D(*GP*GP*GP*TP*AP*TP*AP*CP*GP*C)-3'/ 5'-R(*GP*CP*GP*)-D(*TP*AP*TP*AP*CP*CP*C)-3' BDJ036 H.Yuan, J.Quintana, R.E.Dickerson 5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*CP*G)-3', CALCIUM BDJ037 H.Yuan, J.Quintana, R.E.Dickerson 5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*CP*G)-3',MAGNESIUM BDJ039 U.Heinemann, C.Alings, M.Bansal 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3' BDL038 K.J.Edwards, D.G.Brown, N.Spink, S.Neidle 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3' DDF035 G.A.Leonard, T.Brown, W.N.Hunter 5'-D(*TP*GP*TP*AP*CP*A)-3', 4'-EPIADRIAMYCIN GDL015 K.J.Edwards, T.C.Jenkins, S.Neidle 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3',PENTAMIDINE GDL016 D.G.Brown, M.R.Sanderson, E.Garman, S.Neidle 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3',BERENIL UDL018 C.Kang, X.Zhang, R.Ratliff, R.Moyzis, A.Rich 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3' Coordinates for the following structures have been released: BDL021 J.Aymani, M.Coll, G.A.Van Der Marel, J.H.Van Boom, A.H.-J.Wang, A.Rich 5'-D(CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3'/ 5'-D(CP*GP*CP*GP*TP*T)-3'+ 5'-D(TP*TP*CP*GP*CP*G)-3',MODEL A4 BDL032 J.Aymani, M.Coll, G.A.Van Der Marel, J.H.Van Boom, A.H.-J.Wang, A.Rich 5'-D(CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3'/ 5'-D(CP*GP*CP*GP*TP*T)-3'+ 5'-D(TP*TP*CP*GP*CP*G)-3',MODEL T4 BDJ031 J.R.Quintana, K.Grzeskowiak, K.Yanagi, R.E.Dickerson 5'-D(*CP*GP*AP*TP*TP*AP*AP*TP*CP*G)-3' DDD030 Q.Gao, L.D.Williams, M.Egli, D.Rabinovich, S.-L.Chen, G.J.Quigley, A.Rich 5'-D(*CP*GP*CP*G)-3', DITERCALINIUM GETTING STARTED WITH NDB: ------------------------ If you have never received a newsletter before, send the following 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, 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. NDBQUERY, A SIMPLIFIED USER-INTERFACE: ------------------------------------- We have developed a user-interface program to the database, called "ndbquery", which is designed for the creation of these reports in a friendly and efficient manner. Any subset of structures from the database can be selected, and any features about them can be reported in a formatted table. The format of the tables can be defined by the user, and both ascii and PostScript reports can be generated. THE IMPORTANCE OF REPORTS: ------------------------- Much of the activity on our electronic file server has been obtaining coordinate files for one structure at a time. To take advantage of the full potential of the database, we recommend that you take a look at the available reports. These represent a small sample of the output of the program "ndbquery", which can generate a wide variety of reports, describing any of the stored primary or derived features. The reports are available in both ascii and PostScript formats. We encourage you to retrieve some of the PostScript reports and print them out on a laser printer. You will obtain nicely formatted and easily readable tables, ready for enjoyable scrutiny and display. An example of a more specialized recent report is a table describing the sequences, drug-names, and torsion angles of all intercalated sequences of dinucleotides in the database. This report can be easily made using "ndbquery", by first searching for dimers which have intercalated drugs, and then selecting the sequence, drug name, and the desired torsion angle fields as output options for the report. Another recent query was a search for all B-DNAs which have no mismatches, modifiers, or drugs, and a report of the propeller values for all AA steps occurring in these structures. To explore the potential of the relational database further, we encourage you to get involved in the query making process in one of the following two ways: PERSONALIZED QUERIES: -------------------- Anyone who is interested in creating a report which is not found among the released ones, can receive a report request form by sending the following e-mail message: To: ndblib@helix.rutgers.edu Subject: send queries from newsletter (Note that this is the address of the automatic file server, so the Subject line must exactly look as it appears here for machine readability.) We will create the report, and mail it back via electronic mail. DIRECT ACCESS TO 'NDBQUERY': --------------------------- Our intention is to make the program "ndbquery" generally available to allow direct outside access to the database. In order to develop this, we need to select a few people to test the the program by remotely logging in and making queries (as beta test users). Anyone interested in being considered for this testing process, should request an application form by sending the following e-mail message: To: ndblib@helix.rutgers.edu Subject: send betatest from newsletter ACKNOWLEDGEMENTS: ---------------- 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 (DIR 90 12772). If you use the tables, please use the following citation: 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., In Press.