●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

You can obtain the same instruction information by running TM-score program without argument.

 ./TMscore

 Brief instruction for running TM-score program:
  (For detail: Zhang & Skolnick,  Proteins, 2004 57:702-10)
  
   1. Run TM-score to compare 'model' and 'native':
      >TMscore model native

   2. Run TM-score to compare two complex structures with multiple chains
      (Compare all chains with the same chain identifier)
      >TMscore -c model native

   3. TM-score normalized with an assigned scale d0 e.g. 5 A:
      >TMscore model native -d 5

   4. TM-score normalized by a specific length, e.g. 120 AA:
      >TMscore model native -l 120

   5. TM-score with superposition output, e.g. 'TM.sup':
      >TMscore model native -o TM.sup
      To view superimposed CA-traces by rasmol or pymol:
         >rasmol -script TM.sup
         >pymol -d @TM.sup.p
      To view superimposed atomic models:
         >rasmol -script TM.sup_atm
         >pymol -d @TM.sup_atm.p

   6. Run TM-score based on sequence alignment:
      (This option is only available for C++ version)
      >TMscore -seq model native

./TMscore CA1 CA2

 *****************************************************************************
 *                                 TM-SCORE                                  *
 * A scoring function to assess the similarity of protein structures         *
 * Based on statistics:                                                      *
 *       0.0 < TM-score < 0.17, random structural similarity                 *
 *       0.5 < TM-score < 1.00, in about the same fold                       *
 * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710     *
 * For comments, please email to: zhng@umich.edu                             *
 *****************************************************************************

Structure1: CA1         Length=   71
Structure2: CA2         Length=   73 (by which all scores are normalized)
Number of residues in common=   48
RMSD of  the common residues=    9.411

TM-score    = 0.1480  (d0= 3.00, TM10= 0.1381)
MaxSub-score= 0.1200  (d0= 3.50)
GDT-TS-score= 0.1781 %(d<1)=0.0685 %(d<2)=0.0959 %(d<4)=0.1781 %(d<8)=0.3699
GDT-HA-score= 0.0993 %(d<0.5)=0.0548 %(d<1)=0.0685 %(d<2)=0.0959 %(d<4)=0.1781

 -------- rotation matrix to rotate Chain-1 to Chain-2 ------
 i          t(i)         u(i,1)         u(i,2)         u(i,3)
 1     78.1528787301   0.8174539741   0.0854100234  -0.5696263058
 2     60.9313941247  -0.2092588735  -0.8773351248  -0.4318492822
 3     59.6572072642  -0.5366374234   0.4722162710  -0.6993082791

Superposition in the TM-score: Length(d<5.0)= 14  RMSD=  2.80
(":" denotes the residue pairs of distance < 5.0 Angstrom)
------------------------AAKFESNFNT-QATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSD
                                     :::        :::::    :::   :::                              
LRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGI-----------------------
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