Prime User Manual - ISP

Figure 6.3. The Fold Recognition–Options dialog box.
You may want to turn on Z-scoring if the query protein is any of the following:
• Less than 120 residues long
• More than 90 percent alpha (helical)
• More than 90 percent beta (strand)
Chapter 6: Fold Recognition
Click Options to open the Fold Recognition–Options dialog box and turn on Z-scoring.
Note: Running the search program with Z-scoring on a query with 300 residues typically
requires three to four hours. Without Z-scoring, running a search on a protein of
similar length typically takes only 10-15 minutes.
6.3.2 Search Program Technical Details
The search program finds potential templates for model building by searching a database of
structure folds (SCOP domains) generated from the PDB using secondary structure information.
Profile-sequence matching and composite secondary structure information are the same as in
the Align program used in Edit Alignment in the Comparative Modeling path. The search
program used in the Threading path has two additional features:
• Weighting is adjusted by degree of structural conservation inside a family of templates.
Each residue in the template sequence is defined as conserved or variable according to
Multiple Structure Alignment (MSTRA) of the template with its structural neighbors.
When aligning conserved residues, higher weight is given for matching and higher penalty
is given for opening gaps, and vice versa for variable residues.
• Optional Z-scoring, as described above and discussed in more detail in Section 9.2 on
page 71.
6.3.3 Search Output
When the search is complete, the Templates table displays candidate templates, ranked from
the closest homolog to the least close. This preliminary ranking is based on a scoring function
that combines sequence, secondary structure, and degree of structural conservation. If Zscoring
is on when Search is launched, rankings take Z-score into account as well.
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