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●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

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 spicker3.0.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: spicker_v1.0 was released. In this version, a bug with regard to the input format is fixed. spicker_v1.0 package can be downloaded at release1.0/spicker.tar.gz.
• 2010/08/02: SPICKER V2.0 was released. In this version, 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. spicker_v2.0 package can be downloaded at release2.0/spicker.tar.gz.
• 2010/09/14: modified 'seq.dat' to a simplied format
• 2010/12/29: modified 'rmsinp' to a simplied format
• 2014/01/09: add a license note to 'spicker.f' and modify the instruction part
• 2016/04/21: SPICKER V3.0 was released. In this version, an option was added to cluster decoys using 1/TM-score to replace RMSD as the distance scale. This part is written by Dr. Jens Thomas. spicker_v3.0 package can be downloaded at spicker.tar.gz.

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Reference:
Y. Zhang, J. Skolnick, SPICKER: A Clustering Approach to Identify Near-Native Protein Folds , Journal of Computational Chemistry, 2004 25: 865-871. (download the PDF file).