Information Technology Reference
In-Depth Information
annotate it using an array of options as described in the Cn3D Tutorial
13
. By default,
Cn3D colors the structure according to the secondary structure elements. However,
another useful view is to color the protein by domain (see
Style
menu options), using the
same color scheme as is shown in the graphic display on the Structure Summary page.
These color changes also affect the residues displayed in the Sequence/Alignment
Viewer, allowing the identification of domain or secondary structure elements in the
primary sequence. In addition to Cn3D, users can also display 3D structures with RasMol
or Mage. Structures can also be saved locally as an ASN.1, PDB, or Mage file
(depending on the choice of structure viewer) for later display.
5. Finding and Viewing Structure Neighbors
For an example query on finding and viewing structure neighbors, see Appendix 2
5.1 Why Would I Want to Do This?
x To determine structurally conserved regions in a protein family
x To locate the structural equivalent of a residue of interest in another related
protein
x To gain insights into the allowable structural variability in a particular protein
family
x To develop or test chemical hypotheses regarding an enzyme mechanism
x To predict possible binding sites of a ligand from the location of a binding site in
a related protein
x To identify sites where conformational changes are concentrated
x To interpret mutation studies
x To find areas of conserved positive or negative charge on the protein surface
x To locate conserved hydrophobic or hydrophilic regions of a protein
x To identify evolutionary relationships across protein families
x
To identify functionally equivalent proteins with little or no sequence
conservation.
5.2 How to Begin
The Vector Alignment Search Tool (VAST) is used to calculate similar structures on
each protein contained in the MMDB. The graphic display on each Structure Summary
page (Figure 2) links directly to the relevant VAST results for both whole proteins and
3D domains:
x The 3D Domains link transfers the user to Entrez 3D Domains, showing a list of
the VAST neighbors.
13
[http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtut.shtml]
