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SARST
CPSARST
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SARST: Structural similarity search Aided by Ramachandran Sequential Transformation
Query
(Step 1/3)
PDB/SCOP Entry
*
Format: PDB ID + chain ID.
If there is no chain ID, simply use the
4-letter
PDB ID or use
'_'
to represent the chain.
Multiple entries
are acceptable (batch mode), please use the
comma
to separate them.
Example: 1atpE, 1cewI, 1JUL, 1HEL_, d1swya_, d1oxda_
Local PDB file
Chain ID
*
If there is no chain ID, please leave it
blank
or use
'_'
to represent it.
You can also use
'*'
as the chain ID and then every chain will be used to search the database.
PDB archive
Search
Load Sample
*To perform SARST in this batch mode, please specify a compressed file collecting PDB structures. Acceptable file types: zip, rar, 7z, gz, bz2, tar, tar.gz, tar.bz2 (Maximum size = 16M).
Refinement engine
(Step 2/3)
TM-align (Zhang and Skolnick, 2005)
FAST (Zhu and Weng, 2005)
Target database
(Step 3/3)
Whole PDB (Dec. 2016), 304591 polypeptides
100% identity non-redundant PDB (Dec. 2016), 72603 polypeptides
95% identity non-redundant PDB (Dec. 2016), 39255 polypeptides
90% identity non-redundant PDB (Dec. 2016), 35922 polypeptides
80% identity non-redundant PDB (Dec. 2016), 32611 polypeptides
70% identity non-redundant PDB (Dec. 2016), 30407 polypeptides
50% identity non-redundant PDB (Dec. 2016), 26689 polypeptides
40% identity non-redundant PDB (Dec. 2016), 26037 polypeptides
30% identity non-redundant PDB (Dec. 2016), 25781 polypeptides
25% identity non-redundant PDB (Dec. 2016), 25670 polypeptides
20% identity non-redundant PDB (Dec. 2016), 12614 polypeptides
15% identity non-redundant PDB (Dec. 2016), 8615 polypeptides
10% identity non-redundant PDB (Dec. 2016), 1387 polypeptides
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Whole SCOP (2.06), 215611 domains
100% identity non-redundant SCOP (2.06), 69025 domains
95% identity non-redundant SCOP (2.06), 27862 domains
90% identity non-redundant SCOP (2.06), 25307 domains
70% identity non-redundant SCOP (2.06), 21038 domains
50% identity non-redundant SCOP (2.06), 16657 domains
40% identity non-redundant SCOP (2.06), 13704 domains
35% identity non-redundant SCOP (2.06), 12007 domains
30% identity non-redundant SCOP (2.06), 10266 domains
25% identity non-redundant SCOP (2.06), 8643 domains
20% identity non-redundant SCOP (2.06), 7625 domains
10% identity non-redundant SCOP (2.06), 6820 domains
Class representative SCOP (2.06), 7 domains
Fold representative SCOP (2.06), 1213 domains
Superfamily representative SCOP (2.06), 1995 domains
Family representative SCOP (2.06), 4825 domains
Domain representative SCOP (2.06), 12174 domains
Speices representative SCOP (2.06), 24380 domains
Advanced
Parameters
Hit list size
25
50
100
250
500
1000
2000
3000
E-value cutoff
1e-60
1e-50
1e-40
1e-30
1e-25 (Family-level Significance)
1e-20
1e-15
1e-13 (Superfamily-level Significance)
1e-10
1e-5
1e-3
1e-1
Gap-open (G)/extension (E) Penalty
G=9, E=2 (Highest Accuracy)
G=25, E=2 (Highest Speed)
G=6, E=2
G=7, E=2
G=8, E=2
G=9, E=1
G=10, E=1
G=10, E=2
G=10, E=3
G=11, E=1
G=11, E=2
G=11, E=3
G=12, E=1
G=12, E=2
G=12, E=3
G=13, E=1
G=13, E=2
G=13, E=3
G=14, E=2
G=15, E=1
G=15, E=2
G=16, E=1
G=16, E=2
G=17, E=1
G=18, E=1
G=19, E=1
Structure-based sequence alignment
SE+BLOSUM62
SE+BLOSUM45
None
Start Searching