Prime User Manual - ISP

Prime User Manual
Chapter 8: Maestro Protein Structure Alignment
Chapter 8
It is sometimes useful to be able to align proteins outside the usual Prime workflow. Maestro
provides access to the structure alignment facilities of Prime so that you can perform such
alignments. Two panels are available from the tools menu: the Protein Structure Alignment
panel, and the Align Binding Sites panel.
8.1 The Protein Structure Alignment Panel
To open the Protein Structure Alignment panel, choose Protein Structure Alignment from the
Tools menu in the main window.
In the Protein Structure Alignment panel, structure alignment is performed on Project Table
entries that have been included in the Workspace. The reference structure, whose frame of
reference is used for the alignment, must be the first included entry (the entry with the lowest
row number). To make another protein the reference, move that protein above all the other
included entries in the Project Table.
By default, the alignment includes all residues. However, it is often useful to align a subset of
residues that have greater similarity than the structures as a whole, or are more informative to
compare. Because this program uses matching of secondary structure elements, the subset
should have enough contiguous residues to include at least one helix or strand. Very small
numbers of residues do not produce useful alignments. Selection of subsets is discussed further
under Residues to align, below.
When the alignment calculation is complete, the structures are placed in the same frame of
reference in the Workspace, and the results of the calculation are listed in the text display area
of the Protein Structure Alignment panel. The aligned residues are listed and an RMSD and
Alignment Score are reported. The RMSD is calculated based only on those residues that are
considered to have been successfully aligned, and therefore does not represent an overall
comparison of the structures. It is computed from the C-alpha atoms of the aligned residues.
An Alignment Score lower than 0.6–0.7 indicates a good alignment. Alignment Scores greater
than about 0.7–0.8, or a failure of the structural alignment calculation, indicates there is insufficient
structural similarity for a meaningful alignment. For details on the algorithm, see the
paper by Honig and Yang (J. Mol. Biol. 2000, 301, 665).
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