Prime User Manual - ISP

4.5.2 Align Program Technical Details
Chapter 4: Comparative Modeling: Edit Alignment
The goal of the program launched from the Edit Alignment step, Single Template Alignment,
is to generate an accurate alignment between proteins with medium to high sequence identity
(20-90%). Features of the program include:
• A position-specific substitutional matrix (PSSM) for the query sequence, derived from
PSI-BLAST, is used to match the template sequence.
• In order to minimize the inaccuracy in a single secondary structure prediction, a novel
and robust algorithm has been designed to derive a composite secondary structure for the
query sequence from multiple predictions. The composite SSP is aligned to the SSA of
the template.
4.5.3 Manually Editing the Alignment
You can edit any alignment, however obtained, using combinations of these Prime toolbar
buttons: Slide Freely, Slide as Block, Add(/Remove) Anchors, Lock Gaps, and Unlock Gaps.
Slide Freely (Edit menu): Edit the alignment between query and template. Selecting
a residue and sliding to the right creates N-terminal gaps. Selecting a residue and
sliding to the left creates C-terminal gaps.
Slide As Block (Edit menu): Edit the alignment between query and template.
Selecting a residue and sliding to the right slides all residues as a block to the right.
Selecting a residue and sliding to the left slides all residues as a block to the left.
Add Anchors (Edit menu): Set alignment constraints by setting anchors at residue
positions. To remove anchors, click on the same residue again.
Lock Gaps (Edit menu): To prevent gaps from being collapsed during manual
editing, lock the gaps using this button. Locked gaps are indicated with a - symbol.
Unlock Gaps (Edit menu): To allow gaps to collapse during manual editing, unlock
the gaps using this button. Unlocked gaps are indicated with a ~ symbol.
To assist in this task, you can view a preliminary model of the query in the Workspace. Select
Manual Threading and click Update. The Workspace shows the template structure colored by
query residue property. Each template residue is colored according to the property of the corresponding
query residue in the alignment, revealing the location of charged, polar, and hydrophobic
query residues. Use this option to make sure that insertions/gaps are not in the middle
of regions of secondary structure such as alpha helices or beta sheets. It can also be used to
check that hydrophobic residues point into hydrophobic regions and polar residues point
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