SPICKER is a clustering algorithm to identify the near-native models from a pool of protein structure decoys. You can install and run the SPICKER program at your own computers by

  • 1, download and unpack spicker.tar.gz . This package includes both source code (spicker.f) and executable program (spicker) of SPICKER, as well as other illustration files.
  • 2, Although you can run ./spicker directly, it is recommended that you recompile 'spicker.f' on your computer, which should increase the speed of the program. The suggested compiler include (depending on available compilers in your computer)
    >gfortran -static -O3 -ffast-math -lm -o spicker spicker.f
    or
    >g77 -static -O3 -o -lm spicker spicker.f
For more detail, please read the attached readme file. You can find a set of I-TASSER decoys to test the SPICKER program.

Update history:
  • 2009/01/24: A bug with regard to the input format is fixed
  • 2010/08/02: SPICKER V2.0 is released. A new option is added to automatically tune RMSD cutoff based on variation of decoy distributions. This option works best for decoys generated by ab initio simulations, such as QUARK.
  • 2010/09/14: modified 'seq.dat' to a simplied format
  • 2010/12/29: modified 'rmsinp' to a simplied format
Reference:
Y. Zhang, J. Skolnick, SPICKER: Approach to clustering protein structures for near-native model selection, Journal of Computational Chemistry, 2004 25: 865-871. (download the PDF file).

 


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