NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 12. August 1994. 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: -------------- The current release consists of updated tables describing the 301 three-dimensional structures contained in the database. These include DNA, RNA, and tRNA structures, as well as protein/DNA complexes. Coordinates are available for 231 of these structures. The following new structures, with coordinates, have been added to the database: AHJ052 C.Ban, B.Ramakrishnan, M.Sundaralingam 5'-D(*CP*CP*GP*GP*CP*)-R(*GP*)-D(*CP*CP*GP*G)-3' DDF044 L.A.Lipscomb, M.E.Peek, F.X.Zhou, J.A.Bertrand, D.Vanderveer, L.D.Williams 5'-D(*CP*GP*AP*TP*CP*G)-3', ADRIAMYCIN, -160C DDF045 L.A.Lipscomb, M.E.Peek, F.X.Zhou, J.A.Bertrand, D.Vanderveer, L.D.Williams 5'-D(*CP*GP*AP*TP*CP*G)-3', DAUNOMYCIN, -160C The bibliographic information for the following structures is available: ADH054 S.Kamitori, F.Takusagawa 5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3' AHIB53 W.Cruse, P.Saludjian, E.Biala, P.Strazewski, T.Prange, O.Kennard 5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BR)U)-3' BDJ055 D.S.Goodsell, M.Kaczor-Grzeskowiak, R.E.Dickerson 5'-D(*CP*CP*AP*TP*TP*AP*AP*TP*GP*G)-3' DDDB46 M.E.Peek, L.A.Lipscomb, J.A.Bertrand, Q.Gao, B.P.Roques, C.Garbay-Jaureguiberry, L.D.Williams 5'-D(*(BR)CP*GP*CP*G)-3', FLEXI-DI DDH048 S.Kamitori, F.Takusagawa 5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3', ACTINOMYCIN D GDHB25 X.Chen, B.Ramakrishnan, S.T.Rao, M.Sundaralingam 5'-D(*IP*CP*IP*CP*IP*CP*IP*C)-3', DISTAMYCIN 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 Coordinates for the following structures have been released: ADJ049 B.Ramakrishnan, M.Sundaralingam 5'-D(*CP*CP*CP*GP*GP*CP*CP*GP*GP*G)-3' BDJ052 K.Grzeskowiak, D.S.Goodsell, M.Kaczor-Grzeskowiak, D.Cascio, R.E.Dickerson 5'-D(*CP*CP*AP*AP*GP*CP*TP*TP*GP*G)-3', CALCIUM Coordinates are released only after authorization by the Brookhaven Protein Data Bank. NDB is now available on the World Wide Web: ------------------------------------------ The Nucleic Acid Database file server is now available on the World Wide Web and can be accessed using NCSA's Mosaic W3 browser. An illustrated (HTML-HyperText Markup Language) atlas of all B-DNA structures is available on the NDB W3 server. The atlas provides a quick overview of each structure, containing a ball-and-stick representation of the molecule, along with bibliographic, crystallization, refinement, and coordinate information in a convenient format. The atlas will be extended in the near future to include all the nucleic acid structures in the database. The complete documentation of ndbquery, the interactive Nucleic Acid Database query program, is also available through xmosaic. The ndbquery program itself is not yet accessible to the general public. Here are the simple instructions on how to connect to the NDB W3 server using the Mosaic application: Type the name of the NCSA Mosaic application on your system. On our the computer systems at Rutgers you type: mosaic or xmosaic With the mouse button, click on the word File on the menu bar. Choose Open URL by dragging the pointer down to it. Type the following URL in the pop-up dialog box: http://ndbserver.rutgers.edu:80 Click open. In a few seconds you will see The Nucleic Acid Database home page. Use the scrollbar on the right hand side to move down until you see the following menu. Clicking on any of the underlined items allows you to explore the available information. Notice that after having clicked an underlined item, you will see a new page of information. To move around the page, use the scroll bars on the right hand side and the bottom. Underlined items always indicate further information to be retrieved by clicking on them. To move back to the previous menu, click on the Back button at the bottom left corner. To save any page in your local directory, choose the Save as option from the File menu. ############################################################################### # NDB HTTP Server V3.0 # # # # Welcome to the Nucleic Acid Database (NDB) HyperText Transfer Protocol # # (HTTP) Server. # # # # Each highlighted phrase is a hyperlink to another document or information # # resource of the NDB project. # # # # The following prepared reports summarize some key information about the # # structures contained in the NDB archive: # # # # Names of structures in the NDB archive # # -------------------------------------- # # Primary citations for NDB structures # # ------------------------------------ # # Summary of structure features # # ----------------------------- # # Cell dimensions # # --------------- # # Structures with bound drugs # # --------------------------- # # Structures with modified phosphates # # ----------------------------------- # # Structures with modified bases # # ------------------------------ # # Structures with mismatched base pairs # # ------------------------------------- # # # #The following resources are also available: # # # # NDB Project Newsletters # # ----------------------- # # Preliminary on-line version of the NDBQUERY manual # # -------------------------------------------------- # # An Atlas of B DNA Structures # # ---------------------------- # # The Nucleic Acid Database Gopher Server # # --------------------------------------- # # The Nucleic Acid Database FTP Server # # ------------------------------------ # # # #_______________________________________________________________ # #Nucleic Acid Database Project, Rutgers University, Department of Chemistry, # #New Brunswick, New Jersey # # # ############################################################################### 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 also available via Gopher: ----------------------------- All the information on the NDB file server is also 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 70. On a character terminal based gopher, one would type the following command to connect to the NDB gopher server: gopher ndbgopher.rutgers.edu 70 In addition, the NDB file server can also be accessed through the PDB Internet Gopher. On a terminal running X windows, one could type xgopher to run the X version of 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).