Macromolecular Structure Databases - Essays in Bioinformatics - page 137

x Selecting the chain bar displays the VAST Structure Neighbors page for the entire
chain.
x Selecting a 3D Domain bar displays the VAST Structure Neighbors page for the
selected domain.
5.3 Alternative Points of Entry
x From any Entrez search, select Related 3D Domains to the right of any record
found to view the Vast Structure Neighbors page.
x 5.4 Viewing a 2D Alignment of Structure Neighbors
x A graphic 2D HTML alignment of VAST neighbors can be viewed as follows:
x On the lower portion of the VAST Structure Neighbors page (Figure 3), select the
desired neighbors to view by checking the boxes to their left.
x On the View/Save bar, configure the pull-down menus to the right of the View
Alignment button.
x Select View Alignment .
5.5 Viewing a 3D Alignment of Structure Neighbors
Alignments of VAST structure neighbors can be viewed as a 3D image using Cn3D.
x On the lower portion of the VAST Structure Neighbors page (Figure 3), select the
desired neighbors to view by checking the boxes to their left.
x On the View/Save bar, configure the pull-down menus to the right of the View 3D
Structure button.
x Select View 3D Structure .
Cn3D automatically launches and displays the aligned structures. Each displayed
chain has a unique color; however, the portions of the structures involved in the
alignment are shown in red. These same colors are also reflected in the
Sequence/Alignment Viewer. Among the many viewing options provided by Cn3D, of
particular use is the Show/Hide menu that allows only the aligned residues to be viewed,
only the aligned domains, or all residues of each chain.
6. Finding and Viewing Conserved Domains
For an example query on finding and viewing conserved domains, see Appendix 3.
6.1 Why Would I Want to Do This?
x To locate functional domains within a protein
x To predict the function of a protein whose function is unknown
x To establish evolutionary relationships across protein families
x To interpret mutation studies