Welcome to iSARST Tutorial
Currently 10 threads are running on this PC-cluster.
A typical search along with superimposing 100 structures takes only 3~5 seconds.
Circular permutants can be identified, even when the sequence identity is <10% (Example pair / family).
Please enjoy the speed, accuracy and convenience brought about by iSARST!

Query

5-letter PDB or 7-letter SCOP entry(s):
*
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, 1ti5A, 1JUL, 1HEL_, d1swya_, d1oxda_
Local PDB file:
& Chain ID in this file:
*
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.
Compressed PDB collection:
File type: .zip .rar .tar.gz .tar
* To perform SARST in this batch mode, please specify a compressed file collecting PDB structures,
choose the correct file type, and then click "Submit" (Maximum size = 16M).
Previous session ID:
* Previous searching results can be retrieved by using session ID.

Subject type
Target database
Parameter

Hit list size: E-value cutoff:
Gap-opening (G) and Gap-extension (E) Penalties:

Refinement engine

Structure-based
sequence alignment

Improved by SE+BLOSUM62 SE+BLOSUM45 none


     In this service, we implement two protein structural similarity search methods, SARST and CPSARST.
     Besides, three outstanding structural alignment tools, FAST, TM-align and SAMO, are recruited as refinement engines.
     SE is applied to improve structure-based sequence alignments. We would like to thank these authors for their excellent
     developments, which greatly move this research field forward.

     iSARST allows the user to input many structures at once. Its MPI system will do the similarity searches and
     structural alignments in a batch mode to rapidly retrieve structural homologs of the query proteins.

     SARST is designed for co-linear structural similarity search while CPSARST specifically finds circular permutants.
     Circular permutation (CP)  is a kind of structural rearrangement such that homologous proteins have different
     locations of termini. It is more and more widely used in protein engineering. Please visit CPDB for detailed information.



     How to cite:
     Lo WC, Lee CY, Lee CC, Lyu PC: iSARST: an integrated SARST web server for rapid protein
    structural similarity searches.
     Nucleic Acids Research 2009, 37(Web Server issue):W545-W551; doi:10.1093/nar/gkp291.
     [Abstract] [PDF]
References: Lo WC, Chang CH, Huang PJ, Lyu PC: Protein structural similarity search by Ramachandran codes. BMC Bioinformatics 2007, 8:307. [Abstract] [PDF]
Lo WC, Lyu PC: CPSARST: an efficient circular permutation search tool applied to the detection of
novel protein structural relationships. Genome Biology 2008, 9:R11. [Abstract] [PDF]
>> Other references