Functional diagram of the data management scheme used by the NDB. The figure illustrates the generation of derived structural features by the NDBQuery program using both internal and encapsulated methods. The collections of graphical and tabular reports created by the NDBQuery application are accessible via the NDB network servers.

Example tabular report produced by the NDBQuery program. This report displays the structure descriptor, cell constants, and coordinate status for NDB structures containing the sequence fragment CAATT.

Example tabular report produced by the NDBQuery program. This report displays the citations for structures reported by S. Neidle which contain intercalating drugs.

Example tabular report produced by the NDBQuery program. This report displays the mismatched base pairs and the structure descriptor for NDB structures containing at least one G-G mismatch.

Example histogram charts produced by the NDBQuery program. The distributions of backbone covalent bond angles are shown for B-DNA structures without mismatched base pairs, modifications, or bound drugs.

Example pie charts produced by the NDBQuery program. The distributions of space groups are shown for four nucleic acid conformation types.

Example scatter charts produced by the NDBQuery program. The pair-wise distributions of selected backbone torsions are shown for DNA structures obtained with resolutions better than 1.9Å for three DNA conformation types.

Example torsion ring chart produced by the NDBQuery program. The observed backbone torsions for the Dickerson dodecamer, BDL001 [2] are displayed over a solid cyan band indicating the range of values observed for all B-DNAs in the NDB. The concentric variable shaded regions indicate the one, two and three sigma regions for the distributions of backbone torsions for all B-DNAs in the NDB.

Example molecular graphic produced by the NDBQuery program. Four views of the biological unit of the self-complimentary duplex d(CGATCGATCG) , BDJ025[3].

Example molecular graphic produced by the NDBQuery program. Four views of packing in the unit cell for the self-complimentary duplex d(CGATCGATCG) , BDJ025[3].

The Nucleic Acid Database home page.

The NDB top level query options page. From this menu three query options may be selected: the full WWW NDB query interface, the quick form-based query interface, and the status query Interface. A tutorial describing the use of these query interfaces may also be selected.

The main menu of options for the full NDB query interface. This menu coordinates the structure selection queries and tabular report generation.

The table selection menu provides a list of the table organized in categories according to content. Clicking on a table name from this screen will produce the list of columns in the selected table.

The column selection menu provides a list of the columns in a selected table. Each column is displayed with a description and a few examples.

The condition form allows the user to place a constraint on the value of the column attribute. In this form, the selection condition that the space group be is added to the selection query. This condition on the space group will be appended to the existing selection conditions on the a cell constant which are displayed at the bottom of the form.

This form displays the list of the structures which have been selected by the current selection query. A list of options which can be selected from this form include: the coordinates for the asymmetric unit in mmCIF, PDB and NDB formats, the coordinates for the biological unit in PDB format, the full NDB format entry, the structure of the biological unit viewed using a RASMOL viewer [4], and the coordinates of the biological unit returned to the user with the chemical/x-pdb mime type.

Example display from a structure selection query for NDB structure AHJ043[5] showing the coordinates in mmCIF format and the structure viewed using the RASMOL viewer [4].

An example report created from NDB report preparation interface following a structure selection query. The selection query picked B-DNA structures in space group with an a cell dimension in the range, 23.5 to 24.5 Å. This example report displays the sequences and cell dimensions for the selected structures.

An example illustrating the use of the NDB Quick Query Form to select B-DNA structures determined by author Dickerson, which contains no modifications nor mismatched base pairs, and were determined in space group with resolution better than 1.5 Å.

An example illustrating the use of the NDB status query form to select structures that in being processed at the NDB and are waiting for materials or approval from authors.

An abbreviated NDB status report showing the author and the structure descriptor for NDB structures with status code WAIT. A variety of dates indicating the mile-stones of data processing are available in the status report but are not shown in this figure.

The index page for the NDB Structural Atlas.

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.

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.

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.

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.

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.