NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 10. December 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 ******************************************************************************* ******************************************************************************* @@@@@ @@@@@@@ @ @@@@@ @@@@@@@ @ @ @@@ @@@@@ @ @ @ @ @ @ @ @ @ @@ @ @@@ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @@@@@ @@@@@ @ @ @@@@@ @ @ @ @ @ @ @@@@@ @ @ @@@@@@@ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @@ @ @ @@@@@ @@@@@@@ @ @ @@@@@ @@@@@@@ @ @ @@@@@ @@@@@ @@@@@@ @@@@@@@ @@@@@@@ @@@@@@@ @@@ @ @ @@@@@ @@@@@ @ @ @ @ @ @ @ @ @@ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @@@@ @@@@@@ @@@@@ @@@@@ @ @ @ @ @ @ @@@@ @@@@@ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @@ @ @ @ @ @@@@@ @ @ @@@@@@@ @@@@@@@ @ @@@ @ @ @@@@@ @@@@@ HOPE YOU HAVE HAD A GREAT YEAR! OURS ENDED ON A WONDERFUL NOTE WITH THE ARRIVAL OF SHU-HSIN'S BABY GIRL, INGRID, ON DECEMBER 8. WE, THE NDB STAFF, APPRECIATE THE FEEDBACK FROM OUR DATABASE USERS, AND WE LOOK FORWARD TO LENDING YOU OUR CONTINUED SUPPORT OVER THE NEXT YEAR. PLEASE DO LET US KNOW HOW WE CAN SERVE YOU BETTER. WE WISH YOU ALL THE VERY BEST FOR 1994! 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 248 DNA, RNA, and tRNA structures now contained in the database. Coordinates are available for 192 of these structures. The following new structures, with coordinates, have been added to the database: GDL023 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), PROPAMIDINE C.M.Nunn, T.C.Jenkins, S.Neidle ZDF035 5'-D(*CP*GP*CP*GP*CP*G)-3', SPERMINE, -110C D.Bancroft, L.D.Williams, A.Rich, M.Egli The bibliographic information for the following structures is available: ADJ049 5'-D(*CP*CP*CP*GP*GP*CP*CP*GP*GP*G)-3' B.Ramakrishnan, M.Sundaralingam ADJ050 5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3', ORTHORHOMBIC B.Ramakrishnan, M.Sundaralingam ADJ051 5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3', HEXAGONAL B.Ramakrishnan, M.Sundaralingam BDJ052 5'-D(*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP)-3' K.Grzeskowiak, D.S.Goodsell, M.Kaczor-Grzeskowiak, D.Cascio, R.E.Dickerson GDL014 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3', NETROPSIN L.Tabernero, N.Verdaguer, M.Coll, I.Fita, G.A.Van Der Marel, J.H.Van Boom, A.Rich, J.Aymami Coordinates are released only after authorization by the Brookhaven Protein Data Bank. COORDINATE FILES NOW AVAILABLE IN PDB (BROOKHAVEN PROTEIN DATA BANK) FORMAT: --------------------------------------------------------------------------- All the coordinates that had been available in NDB format are now also available in PDB format. These files are located in the directory called coord_pdb. To obtain a coordinate file in PDB format send the following mail message: To: ndblib@ndbserver.rutgers.edu Subject: send from coord_pdb where the word is replaced by the desired file name. The name of each file in this directory is the same as its NDB file name (NDB ID) with the .pdb extension added. For example, the PDB-format coordinate file for the structure bdl001 is called bdl001.pdb. For structures with only one strand per asymmetric unit, the coordinates for the complete double helix are available in a second file, with an 's' added to the file name. For example, structure adh008 has two PDB coordinate files: adh008.pdb and adh008.pdbs. For more information and a complete list of coordinate files available in this directory, please send the following mail message: To: ndblib@ndbserver.rutgers.edu Subject: send index from coord_pdb The PDB-format coordinate files can be accessed via anonymous ftp and gopher in the usual manner, by going to the directory coord_pdb. STATUS OF BETA TEST: ------------------- We discussed in an earlier newsletter the beta test of the Nucleic Acid Database query application, ndbquery. Currently, the beta test version of the 'ndbquery' program is being tested by seven scientists who wished to participate in the NDB beta test. UPCOMING EVENTS: --------------- We are currently processing DNA/Protein complexes. They will be available for public use soon. 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. 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. 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).