Prime User Manual - ISP

Alignment Section
Chapter 8: Maestro Protein Structure Alignment
Gap penalty
In the structure alignment calculation, this is the alignment score penalty for initiating a gap in
the alignment. The default gap penalty is 2.00. The main purpose of this parameter is to
prevent the generation of very poor initial alignments.
Deletion penalty
In the structure alignment calculation, this is the penalty for extending a gap. The default deletion
penalty is 1.00.
Secondary Structure Section
Use scanning alignment
This option is deselected by default. When it is selected, structure alignment is carried out in
scanning rather than the default global mode. Generally, the default global mode is more
useful. However, if you do not find any similarity between structures with global alignment,
you can try scanning alignment.
Global alignment involves running double dynamic programming on the full scoring matrix
built from all secondary structural elements (SSEs) in both structures. In scanning alignment
double dynamic programming is run on successively smaller subregions of the full scoring
matrix (window sizes of 20, 15, 10 and 5 SSEs) until a reasonable alignment is produced.
Assuming a reasonable alignment is found it is used as a starting point for building a global
alignment (involving all SSEs).
Window length
Number of successive SSEs that are to be used as a baseline for the global alignment. The
default is 5. This option is significant only if Use scanning alignment has been selected.
Minimum similarity
This is the alignment score above which alignments are reported as unsuccessful. The default
is 1.00, where alignment scores of 0.7 or less mean greater similarity, and alignment scores
above 1.0 mean less similarity. When alignment scores are greater than 1.0, the alignment is
unlikely to be meaningful.
Structural similarity of proteins is measured by the Protein Structural Distance (PSD). This
measure combines the similarity scores for the secondary structural elements obtained from
dynamic programming and the RMSD of aligned residues for the optimal alignment. For
details see Yang, A.; Honig, B. Journal of Molecular Biology 2000, 301, 665-678.
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