Section 24.2.5. Data distribution

The NDB archives, a section of the web site, contain a large variety of information and tables useful for researchers. Prepared reports about the structure identifiers, citations, cell dimensions and structure summaries are available and are sorted according to structure type. The dictionaries of standard geometries of nucleic acids as well as parameter files for X-PLOR (Brünger, 1992) are also available. The archives section links to the ftp server, providing coordinates for the asymmetric unit and biological units in PDB and mmCIF formats, structure-factor files, and coordinates for nucleic acid structures determined by NMR.

A very popular and useful report is the NDB Atlas report page. An Atlas page contains summary, crystallographic and experimental information, a molecular view of the biological unit and a crystal-packing picture for a particular structure. Atlas pages are created directly from the NDB database (Fig. 24.2.5.1). The Atlas entries for all structures in the database are organized by structure type on the NDB web site.

Figure 24.2.5.1| top | pdf | NDB Atlas page for URX035 (Scott et al., 1995) that highlights structural information that is contained in the database and provides images of the biological unit, asymmetric unit and crystal packing of the structure.

A web interface was designed to make the query capabilities of the NDB as widely accessible as possible. To highlight the special features of NDB, the interface operates in two modes. In the quick search/quick report mode, several items, including structure ID, author, classification and special features, can be limited either by entering text in a box or by selecting an option from the pull-down menu. Any combination of these items may be used to constrain the structure selection. If none are used, the entire database will be selected. After selecting `Execute Selection', the user will be presented with a list of structure IDs and descriptors that match the desired conditions. Several viewing options for each structure in this list are possible. These include retrieving the coordinate files in either mmCIF or PDB format, retrieving the coordinates for the biological unit, viewing the structure with RasMol (Sayle & Milner-White, 1995), or viewing an NDB Atlas page.

Preformatted quick reports can then be generated for the structures in this results list. The user selects a report from a list of 13 report options (Table 24.2.5.1), and the report is created automatically. Multiple reports can be easily generated. These reports are particularly convenient for being able to produce reports quickly based on derived features, such as torsion angles and base morphology (Fig. 24.2.5.2).

Table 24.2.5.1| top | pdf | Quick reports available from the NDB Report name Contents NDB status Processing status information Cell dimensions Crystallographic cell constants Primary citation Primary bibliographic citations Structure identifier Identifiers, descriptor, coordinate availability Sequence Sequence Nucleic acid sequence Nucleic acid sequence only Protein sequence Protein sequence only Refinement information R factor, resolution and number of reflections used in refinement Nucleic acid backbone torsions (NDB) Sugar–phosphate backbone torsion angles using NDB residue numbers Nucleic acid backbone torsions (PDB) Sugar–phosphate backbone torsion angles using PDB residue numbers Base-pair parameters (global) Global base-pair parameters calculated using Curves 5.1 (Lavery & Sklenar, 1989) Base-pair step parameters (local) Local base-pair step parameters calculated using Curves 5.1 Groove dimensions Groove dimensions using Stoffer & Lavery definitions from Curves 5.1

Figure 24.2.5.2| top | pdf | Examples of quick reports. Clockwise from top left: base-pair parameters [global; calculated using Curves 5.1 (Lavery & Sklenar, 1989)] report for ribozyme structures; nucleic acid backbone torsions (NDB) report for ribozyme structures; structure identifier report for protein–DNA structures; citation report for protein–DNA structures.

In the full search/full report mode, it is possible to access most of the tables in the NDB to build more complex queries. Instead of limiting items that are listed on a single page, the user builds a search by selecting the tables and then the items that contain the desired features. These queries can use Boolean and logical operators to make complex queries.

After selecting structures using the full search, a variety of reports can be written. The report columns are selected from a variety of database tables, and then the full report is automatically generated. Multiple reports can be generated for the same group of selected structures; for example, reports on crystallization, base modification, or a combination of these reports can be generated for a particular group of structures.

The NDB is based at Rutgers University (http://ndbserver.rutgers.edu/ ) and is currently mirrored at three other sites: the Institute of Cancer Research (ICR) in London, England (http://www.ndb.icr.ac.uk), the San Diego Supercomputer Center in San Diego, USA (http://ndb.sdsc.edu/NDB/) and the Structural Biology Centre in Tsukuba, Japan (http://ndbserver.nibh.go.jp/NDB/). These mirror sites are updated daily, are fully synchronous, and contain the ftp directories, the web site and the full database.