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Initial superimposition

The structure comparison algorithm of Argos & Rossmann [3], which is the method used by STAMP, requires that the protein structures being compared are approximately superimposed initially. If not then structural similarity may be undetected, and reliable superimpositions and alignments unattainable. This is a very important thing to remember about STAMP. If initial superimpositions do not yield high enough scores (i.e. $S_{c} < 2.0$) or if the structures are generally different, STAMP will warn you by printing `LOW SCORE' warnings in its output.

The STAMP package provides three methods of arriving at an initial superimposition. The first of these is to make use of an alignment derived on the basis of sequence. The program ALIGNFIT requires that the sequences extracted from the PDB files (using the program PDBSEQ) are aligned vertically in AMPS block format (see format and examples below); one can use AMPS or another method of aligning sequences. The ACONVERT program is included in the distribution to faciliate converting alignments to AMPS format from other formats; it also possible to use Jalview (www.jalview.org) to perform the conversion. STAMP compares all possible pairs of structures by performing a least squares fit on all equivalenced $C_{\alpha}$ atoms. Once all pairwise comparisons are compared, the program makes use of a tree to superimpose multiply all coordinates following the tree. Thus the final superimposition output is the best possible fit of the structure given the alignment. For an example where ALIGNFIT is used to provide an initial superimposition, refer to the alignment of the serine proteinases in Chapter 2.

In instances where multiple sequence alignment is inaccurate, ALIGNFIT may still be used, though the initial superimpositions may not be accurate enough for STAMP to find structural similarity. In such cases, the best way to arrive at initial superimpositions is to use the SCAN option within STAMP. This option compares a query domain against a database of target domains and generates a set of superimpositions of the target domains onto the query domain. This set of superimpositons constitutes a multiple aligment that can be used by STAMP as an initial alignmnent. This works particularly well when structures are very diverse. For an example, see the alignment of the aspartyl proteinase N- and C- terminal lobes in Chapter 2.


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Next: Pairwise comparisons and alignments Up: A brief description of Previous: A brief description of   Contents