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A brief instruction for running TM-score program:

(For detail, please see Y Zhang, J Skolnick, Proteins, 2004 57: 702)


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. TM-score normalized with an assigned scale d0 e.g. 5 A: >TMscore model native -d 5 3. TM-score normalized by a specific length, e.g. 120 AA: >TMscore model native -l 120 4. TM-score with superposition output, e.g. 'TM.sup': >TMscore model native -o TM.sup To view the superimposed CA-traces by rasmol: >rasmol -script TM.sup To view superimposed atomic models by rasmol: >rasmol -script TM.sup_atm
Following is an example of running TM-score
    ./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----------------------- 123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456
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