In addition to the query interfaces, the NDB also provides a variety of other network resources. A Structural Atlas of nucleic acids developed by the NDB provides a summary of the essential experimental and structural features for each for the structures in the NDB. An Atlas entry includes links to coordinate data files and graphic illustrations of the biological unit and unit cell packing for each structure. The information in the Atlas is generated as a report from the NDBQuery application. Images in the atlas can be generated automatically using NDBQuery (Figures 9 and 10) or selected from a repository of manually prepared images (Figures 25 and 26). The index for the Web version of the Atlas is shown in Figure 23, and an example Atlas entry is shown in Figures 24 - 26.
The NDB maintains an archive containing coordinate data files, standard reports describing the current contents of the NDB, dictionaries of nucleic acid standard geometries and parameter files, on-line documentation, software and project newsletters. This archive is available via ftp or through a Web interface. The Web index for the NDB archive is shown in Figure 27.
The NDB is also the primary network site for information related to the development of the macromolecular CIF (mmCIF) dictionary and DDL. The mmCIF home page is shown in Figure 28. The mmCIF archive site contains a variety of introductory and historical information about the mmCIF and DDL development effort, and the latest text and HTML versions of the mmCIF and DDL dictionaries. Information about software tools for mmCIF and several mail reflectors on mmCIF topics are also archived at this site.
Figure 23:
The index page for the NDB Structural Atlas.
Figure 24:
An atlas entry for the B-DNA dodecamer structure, BDL001 [2]. This page of the
atlas gives the structure type, compound name, sequence, citation, space group, cell constants,
crystallization conditions and refinement data. Links are provided to coordinate data,
images of the biological unit, and images of packing in the unit cell for this structure.
Figure 25:
A molecular graphic from from the NDB Atlas entry for the B-DNA dodecamer structure,
BDL001 [2]. This ball and stick representation is color coded by sequence.
Figure 26:
A molecular graphic from from the NDB Atlas entry for the B-DNA dodecamer structure,
BDL001 [2]. This space filling representation of the unit is color coded
in terms of the symmetry related molecules.
Figure 27:
The Archives page provides links to a variety of information that is routinely
updated by the NDB. This includes collections of standard reports describing
the current contents of the NDB, dictionaries of nucleic acid standard geometries and
parameter files, on-line documentation, project newsletters, and links to the NDB FTP archive.
Figure 28:
The macromolecular CIF (mmCIF) home page. The information which can be accessed from
this page includes: the history of the development of the mmCIF
dictionary and Dictionary Description Language (DDL), the text and HTML versions of
the mmCIF and DDL dictionaries, descriptions of mmCIF software tools, and related
mailing lists.