NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 6. December 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 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 KINEMAGE FILES: --------------- The user-interface program to the Nucleic Acid Database has been extended to produce kinemage files (kinetic images) for the structures contained in NDB. Kinemages for all unbound B-DNAs are now available on the file server in the directory called kinemage. Kinemages, developed by the Jane and David Richardson of Duke University, are scientific illustrations of three-dimensional structures viewed on Apple Macintosh computers. The structures are shown in an interactive display, which allows the viewer to rotate the structures, turn certain parts on or off, identify points, and animate between different forms. The kinemages are distributed as plain text files, and are viewed on the Macintosh with the program MAGE. Please refer to the following article for a more detailed description of kinemages. A copy of the program MAGE is also available with this publication. David C. Richardson and Jane S. Richardson. 1992. The kinemage: A tool for scientific communication. Protein Science, 1, 3-9. We are pleased to report that the Biophysical Journal is now also publishing kinemages. A sampling of DNA dodecamer kinemages produced by the Nucleic Acid Database, together with the program MAGE, has been published in the November issue: H. M. Berman, W. K. Olson, J. S. Richardson, J. D. Westbrook. 1992. Natour1: A sampling of DNA dodecamer structures. A kinemage. Biophysical J., 63, Diskette Appendix to No. 5. The kinemage files available on the NDB file server are also plain text files, which can be transferred to a Macintosh computer and viewed by the program MAGE. We look forward to a new version of MAGE running on PCs. The kinemage files are located in the directory called kinemages. To get a complete list of these files, send the following e-mail message: To: ndblib@helix.rutgers.edu Subject: send index from kinemages To get a kinemage file itself, send this message, substituting the word by the name of the desired kinemage file as described in the index. To: ndblib@helix.rutgers.edu Subject: send from kinemages Note that the kinemage files have file names of the form .kin, where is replaced by the NDB name of the structure. NEW STRUCTURES: -------------- Since October, six 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 210 DNA, RNA, and tRNA structures now contained in the database. Coordinates are available for 137 of these structures. The following new structures have been added to the database: BDL040 J.C.Xuan, I.T.Weber 5'-D(*CP*GP*CP*IP*AP*AP*TP*TP*CP*GP*CP*G)-3' BDL041 G.A.Leonard, E.D.Booth, W.N.Hunter, T.Brown 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*IP*GP*CP*G)-3' BDLB33 G.A.Leonard, A.Guy, T.Brown, R.Teoule, W.N.Hunter 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(O)AP*GP*CP*G)-3' GDLB19 M.Sriram, G.A.van der Marel, H.L.P.F.Roelen, J.H.van Boom, A.H.-J.Wang 5'-D(*CP*GP*CP*(E)GP*AP*AP*TP*TP*CP*GP*CP*G)-3',HOECHST 33258 GDLB20 M.Sriram, G.A.van der Marel, H.L.P.F.Roelen, J.H.van Boom, A.H.-J.Wang 5'-D(*CP*GP*CP*(E)GP*AP*AP*TP*TP*CP*GP*CP*G)-3',HOECHST 33342 GDL021 M.Sriram, G.A.van der Marel, H.L.P.F.Roelen, J.H.van Boom, A.H.-J.Wang 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', HOECHST 33342 Coordinates for the following structures have been released: 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' DDB004 S.E.Sherman, D.Gibson, A.H.-J.Wang, S.J.Lippard 5'-D(*P*GP*G)-3', CISPLATIN 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 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 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 the automatic file server: To: ndblib@helix.rutgers.edu Subject: send betatest from newsletter ACKNOWLEDGEMENTS: ---------------- The following article describing the Nucleic Acid Database project has 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. From now on, 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).