Prime User Manual - ISP

Chapter 11: Command Syntax
The following input file, assumed to be called all-methods.inp, instructs the ssp script to
produce secondary structure prediction for all methods available—SSPro and, depending on
the local installation, PSIPRED.
QUERY_FILE query.fasta
METHOD all
11.8 sta—Single Template Alignment
The Single Template Alignment (STA) program in PRIME is designed for protein sequences
with medium to high sequence identity (>25%). STA differs from standard sequence alignment
such as BLAST by taking into account secondary structure matching as well as profilesequence
matching. As a result, STA often generates better alignment than BLAST in the
regions where sequence conservation is relatively weak. STA can also take in constraints, such
as user-selected residue pairs to be aligned together and/or residues in either query or template
that are not to be aligned (gaps).
STA can use templates directly from the PDB, as selected by running the Find Homologs step,
and can also use templates from the Prime fold library, as selected in the Fold Recognition
step. For the latter, you can export the template from the Fold Recognition table, and save it as
a PDB file.
Syntax
$SCHRODINGER/sta [options] jobname
The input is read from the file jobname.inp and the output is written to jobname.out.
Options
The sta script accepts the -DEBUG and -HOST options, as described in Table 11.1.
Command Input File
The input file consists of lines containing keyword-value pairs, one per line. The keywords are
described in Table 11.11.
Files
• Input file—named jobname.inp. Contains keywords for running the program.
• Query sequence file—File containing the complete sequence of the query, in FASTA format.
Specified in the input file.
• Secondary structure prediction files in CASP format for the query sequence. See page 93
for an example of CASP format.
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