The NDBQuery application provides a query interface to the NDB. This application guides the user in the creating complex selection queries on the NDB through a series of interactive menus. The application is designed to help the user select a collection of structures satisfying a set of conditions which may be placed on either primary or derived structural features. The application then guides the user in retrieving information related to the group of selected structures.
NDBQuery provides a variety of output options. The form of output is simply the retrieval of coordinates for selected structures in a format such as PDB or mmCIF. Tabular reports can be created in formatted ASCII text files and also using the more sophisticated formatting features provided by LaTeX. Some example reports produced by the NDBQuery program are shown in Figures 2 - 4. NDBQuery creates graphical reports in a variety of different formats. Some examples of these graphical reports include the histogram charts shown in Figure 5, the scatter charts shown in Figure 7, the pie charts Figure 6, the torsion ring plots shown in Figure 8, and molecular graphics shown in Figures 9 and 10. All of the query and report generation operations performed by the NDBQuery program can be saved in script files enabling very complicated queries and reports to be processed in a single command, without the aid of the user interface.
Figure 2:
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.
Figure 3:
Example tabular report produced by the NDBQuery program. This report displays
the citations for structures reported by S. Neidle which contain intercalating
drugs.
Figure 4:
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.
Figure 5:
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.
Figure 6:
Example pie charts produced by the NDBQuery program. The distributions of space groups are
shown for four nucleic acid conformation types.
Figure 7:
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.
Figure 8:
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.
Figure 9:
Example molecular graphic produced by the NDBQuery program. Four views of the biological unit
of the self-complimentary duplex d(CGATCGATCG) 
, BDJ025[3].
Figure 10:
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].