One-against-all All-against-one
All-against-one search is more time-consuming but sometimes much more sensitive.
Users interested in hypothetical proteins, such as 1PUJ (chain A), may try all-against-one mode.

Word Size: 2 (recommended) 3 (faster)
Gap-opening (G) and Gap-extension (E) Penalties: G=25, E=2 (fastest) G=6, E=2 G=7, E=2 G=8, E=2 G=9, E=1 G=9, E=2 G=10, E=1 G=10, E=2 G=10, E=3 (recommended) 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

Sequence identity improvement: >-10% >-5% >-2.5% Disabled >0% >5% >10% >15% >20% >25% >30%
Definition of sequence identity: A: number of identical residues aligned B: A/(alignment size) C: A/(protein size)
Permutation size limit: >= 5% >= 10% >= 15% >= 20% >= 25% >= 30% >= 35% >= 40% >= 45% and < 50%
Structural similarity improvement: >10% >15% >20% >25% >30% >35% >40% >45% >50%
CP score threshold: (range: 0.0 ~ 1.0)
RMSD cutoff:

References:
     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] (Published: Jan. 18th, 2008)

     Lo WC, Chang CH, Huang PJ, Lyu PC: Protein structural similarity search by Ramachandran codes.
     BMC Bioinformatics 2007, 8:307.
     [Abstract] [PDF] (Published: Aug. 23th, 2007; Website: http://sarst.life.nthu.edu.tw)

Authors:
  Wei-Cheng Lo and Ping-Chiang Lyu,
  Institute of Bioinformatics and Structural Biology, National Tsing Hua University,
  Taiwan, R.O.C.

Downloads:
  1.Stand-alone Java Version (CPSARST.tar.gz, CPSARST.zip)
    This program can work on any platform with Java(TM) 2 runtime environment.
    java version: 1.4 or latter

  2.Screening engine, bl2seq: http://www.ncbi.nlm.nih.gov/BLAST/download.shtml

  3.Refinement engine, fast: http://biowulf.bu.edu/FAST/download.htm

Supplementary data files:
  1.nrPDB-90
  2.nrSCOP-90
  3.Candidate CP pairs in nrPDB-90 (we have submitted this file to the journal)
  4.Structural neighbors of YlqF retrieved by DALI
  5.Statistics of protein structural database searches with broad criteria
  6.A collection of 20,000 random circular permutants

Acknowledgement:
     FAST (FAST Alignment and Search Tool) is used as the refinement engine in this
  service. We thank Jianhua Zhu and Zhiping Weng for their generous support.


Note:

     The stand-alone CPSARST requires "bl2seq" and "fast" to function properly,
  please download them along with CPSARST.