Hit list size: 25 50 100 250 500 E-value Cutoff: 1e-25 (Family-level Significance) 1e-20 1e-15 1e-13 (Superfamily-level Significance) 1e-10 1e-7 1e-5 1e-3 1e-1 1e0 1e1 1e2 1e3
Gap-opening (G) and Gap-extension (E) Penalties: 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
Enable Score Normalization Enable RMSD Calculator

Reference:
     Lo WC, Chang CH, Huang PJ, Lyu PC: Protein structural similarity search by Ramachandran codes.
     BMC Bioinformatics 2007, 8:307.
     [Abstract] [PDF]

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

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

  2.Ramachandran Sequence Databases for ASTRAL SCOP 1.69 (SARSTdb_SCOP169s.tar.gz, SARSTdb_SCOP169s.zip)

  3.Ramachandran Sequence Database for PDB 2006 (SARSTdb_PDB2006.tar.gz, SARSTdb_PDB2006.zip)


Acknowledgement:
     FAST (FAST Alignment and Search Tool, http://biowulf.bu.edu/FAST/)
  is used to calculate the RMSD in this service. We thank Jianhua Zhu
  and Zhiping Weng for their generous support.


Note:
     The standalone version recruits "blastall" as the search engine,
  which can be found in the BLAST executables packages. If you need
  blastall, please refer to NCBI BLAST download page:
  http://www.ncbi.nlm.nih.gov/BLAST/download.shtml