// \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ // THE NUCLEIC ACID DATABASE NEWSLETTER Number 21. March 1997. All of the NDB developments and projects discussed in this newsletter are available through the WWW site (http://ndbserver.rutgers.edu) and its mirror sites (http://www.ebi.ac.uk/NDB/ and http://ndbserver.nibh.go.jp/NDB/). Comments, queries, and questions about NDB and this newsletter should be sent to ndbadmin@ndbserver.rutgers.edu. -------------------------------- Contents -------------------------------- New NDB Mirror NDB WWW Full Interface: New Report Generation Features NDB WWW Interfaces: Tutorials and Suggestions Protein Finder Ligand Database Zukang Feng Summer Program Musical Atlas -------------------------------- New NDB Mirror -------------- We are pleased to announce that the NDB is now mirrored at the Structural Biology Centre at AIST-NIBH in Tsukuba, Japan. The address is http://ndbserver.nibh.go.jp/NDB/. Our liason at AIST-NIBH is Professor Masashi Suzuki, the director of the center. This site mirrors the NDB home site at http://ndbserver.rutgers.edu/, and will be updated regularly along with the original NDB mirror at the European Bioinformatics Institute at http://www.ebi.ac.uk/NDB/. NDB WWW Full Interface: New Report Generation Features ------------------------------ The NDB has added new features that can be included in reports generated from the WWW Full Interface. These report features include: * Base morphology parameters as calculated by the program Curves 5.1(1). * Non-bonded contacts ranging from 0 to 3 Angstroms. * Secondary structure descriptions for proteins (such as helix, sheet, turn, SS bond). * The symmetry operations needed to create the full biological unit or portions of it. * The different chemical types in the structure including names and numbers of the polymer and non-polymer structures found in the asymmetric unit. Reports can be generated by using the NDB Full Interface on the NDB WWW site. Information on interface tutorials and creating reports is found below. (1)R. Lavery, H. Sklenar, Curves 5.1. Helical Analysis of Irregular Nucleic Acids, Institute de Biologie Physico-Chimique, Paris, 1996. NDB WWW Interfaces: Tutorials and Suggestions ------------------------- The tutorials available on-line for the different NDB WWW Interfaces have been updated and revised. These new examples reflect the changes made in the database, and now provide more detailed examples of what kinds of searches and reports are possible. These tutorials are available along with the three interfaces on the main "Searching the database" page. The new tutorials also include interface overviews, a troubleshooting guide, and the following tips for report generation: +The report will automatically include the NDB Structure ID as the first column. +When creating reports, the row order in the report is first determined by the NDB ID. For reports where there are multiple rows for each structure (such as in the table sugar_phosphate_geometry), the report is then further ordered by the first column selected. +Multiple columns will take longer to generate, especially for a large number of structures. +The reports generated can be saved and edited. For best results, use the "Save As...Text" option available from the "File" option on the browser menu (where available). Protein Finder -------------- The NDB is also pleased to announce the release of a new WWW query interface called Protein Finder. The Protein Finder database is a relational database which contains structural and experimental information for protein structures found in the Protein Data Bank (PDB). The simple WWW interface provided by Protein Finder permits the user to construct complex selection queries, prepare tabular reports, view/retrieve coordinate files, or view molecular structures using RASMOL. The Protein Finder database is created and maintained in a completely automated fashion using the same set of software tools that were originally developed for primary data processing of oligonucleotide structures by the Nucleic Acid Database Project (NDB). These tools process the information from the protein data files and load this information into a relational database. At this time, the content of the Protein Finder database is extracted from the data files in the PDB archive without modification. The database is currently available at the Rutgers Site and will shortly be available at all of the NDB mirror sites. Ligand Database --------------- We have recently created an automated procedure for constructing models of ligands associated with macromolecules in the Nucleic Acid Database (NDB) and the Protein Data Bank (PDB). This work was presented by John Westbrook at the Protein Ligand Databases Workshop at EBI in December 1996. Zukang Feng ----------- Zukang Feng has settled into his work here at the NDB and has worked on our program MAXIT, which is our primary and very versatile data processing tool. Zukang, who formerly worked at the Roswell Park Cancer Institute in Buffalo, NY and prior to that worked with Manfred S. Sippl at Salzburg University, will be working at the NDB on structure comparison. Summer Program -------------- Preparations are underway for another summer of undergraduate research. Past summer projects have included the NDB Pictorial and Musical Atlases, and mmCIF software programs. Musical Atlas ------------- One of our undergraduate summer projects last year was the creation of a Musical Atlas that provided aural representations of sequence for selected B-DNA structures. A new algorithm has been created by Gautam Malhotra (Rutgers University, '96) which creates compositions representing more detailed aspects of structure for A-, B-, and Z-DNA. This Atlas and a detailed explanation of this project are available through the Archives section of the NDB home page. Please note that you will need hardware and software that allows you to listen to .AU and .WAV files to hear these compositions. ******************************************* Researchers who wish to use information obtained from NDB should 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., 63, 751-759. The Nucleic Acid Database Project is funded by the National Science Foundation and the Department of Energy // \\ // \\ // \\ // \\ // \\ // \\ // \\ \\': | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | \\ \\ | :,\\' | // \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\ \\ // \\ // \\ // \\ // \\ // \\ // \\ //