Prime User Manual - ISP

Prime User Manual
Chapter 4
Chapter 4: Comparative Modeling: Edit Alignment
4.1 The Comparative Modeling Path
In the initial steps of Prime–SP, you imported a query sequence (Input Sequence) and identified
possible templates (Find Homologs). If a query-template match with a substantial
percentage of identical residues has been selected, it is appropriate to continue the structure
prediction process by following the Comparative Modeling path, a series of two Prime–SP
steps used to build a model structure of the query sequence based on homology to one or more
templates.
The structure prediction process in the Comparative Modeling path includes the following
steps:
1. A satisfactory query-templates sequence alignment is produced in Edit Alignment.
2. The selected query-template alignment is used to build a model structure of the query in
Build Structure.
4.2 Overview of the Edit Alignment Step
In order to build a model structure of the query, the Build Structure step requires a satisfactory
alignment between templates and query. The alignment of templates to query generated in the
Find Homologs step is based only on sequence. Therefore, there is room for improvement. The
Edit Alignment step allows you to improve alignments using various tools before building a
model in the Build Structure step.
There are several ways to produce an alignment for use in Build Structure:
• Accept the BLAST/PSI-BLAST alignment generated in the Find Homologs step and currently
displayed in the sequence viewer.
• Import an alignment.
• Generate or import secondary structure predictions, then use the Align program to create
a new alignment.
• Edit any of these alignments manually.
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