PREDATOR
2.1.2
Protein secondary structure prediction from a single sequence or a set of sequences
D. Frishman & P. Argos
Frishman, D. and Argos, P. (1996) Incorporation of long-distance interactions into a secondary structure prediction algorithm. Protein Engineering, 9, 133-142.
Frishman, D. and Argos, P. (1997) 75% accuracy in protein secondary structure prediction. Proteins, 27, 329-335.
Frishman,D and Argos,P. (1995) Knowledge-based secondary structure assignment. Proteins: structure, function and genetics, 23, 566-579.
Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22: 2577-2637.
protein:2d structure
predator
predator
perl
"predator"
0
seq
Protein sequence(s) File
perl
" $value"
100
8
100
15
seqsfile
perl
1
prediction
Prediction options
1
single
Perform single sequence prediction. Ignore other sequences in the set for computing the prediction (-s)
perl
($value)? " -s" : ""
0
1
perl
!$all
dont_copy
Do not copy assignment directly from the PDB database (-u)
perl
($value)? " -u" : ""
0
1
Do not copy assignment directly from the PDB database if query sequence is found in PDB. By default, the known conformation of 7-residue segments will be used if they are identical to a 7-residue fragment in the query sequence.
dssp
Use DSSP target assignment (-d)
perl
($value)? " -d" : ""
0
1
Use DSSP target assignment (default is STRIDE). The predictions made with DSSP and STRIDE target assignments are optimized to reproduce these assignments as well as possible.
perl
$dssp_file
percentid
Find a subset of sequences with no more than this identity between any pair of sequences (-n)
perl
(defined $value)? " -n$value" : ""
1
input
Input parameters
1
all
Make prediction for All sequences in the input file (-a)
perl
($value)? " -a" : ""
0
1
perl
!$seqid
seqid
Make prediction for this sequence (give its id) (-i)
perl
($value)? " -i$value" : ""
1
This option is case sensitive!
stride_file
STRIDE file (-x)
perl
($value)? " -x$value" : ""
1
stride_outfile
perl
1
dssp_file
DSSP file (-y)
perl
($value)? " -y$value" : ""
1
dssp_outfile
perl
1
pdb_chain
PDB Chain (-z)
perl
($value)? " -z$value" : " -z-"
1
perl
$dssp_file || $stride_file
output
Output parameters
1
long
Long output form (-l)
perl
($value)? " -l" : ""
0
1
Every output line contains residue number, three-letter residue name, one-letter residue name, predicted secondary structural state and reliability estimate. If a STRIDE or DSSP secondary structure assignment has been read (see other options), the known assignment will also be shown in the output for comparison. By default the short output form is used.
other_info
Output other additional information if available (-h)
perl
($value)? " -h" : ""
0
1