●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

Brief instruction (you can obtain the same information by running MM-align program without argument)

 Brief instruction for running MM-align program:
 (For detail: Mukherjee & Zhang, Nucl. Acid. Res. 37:e83, 2009)

 Please make sure that the two chains of both complexes are seperated by a "TER".

 1. Align 'complex1.pdb' to 'complex2.pdb'
   (By default, TM-score is normalized by the length of 'complex2.pdb')
   >MMalign complex1.pdb complex2.pdb

 2. Run MM-align and output the superposition to 'MM.sup' and 'MM.sup_all':
   >MMalign complex1.pdb complex2.pdb -o MM.sup
    To view the superimposed structures of the aligned regions by rasmol:
   >rasmol -script MM.sup
    To view the superimposed structures of all regions by rasmol:
   >rasmol -script MM.sup_all

 3. If you want TM-score normalized by an assigned length, e.g. 100 aa:
   >MDMalign complex1.pdb complex2.pdb -L 100
    If you want TM-score normalized by the average length of two structures:
   >MMalign complex1.pdb complex2.pdb -a
    If you want TM-score normalized by the shorter length of two structures:
   >MMalign complex1.pdb complex2.pdb -b
    If you want TM-score normalized by the longer length of two structures:
   >MMalign complex1.pdb complex2.pdb -c

 4. If you want MM-align to enforce interface alignment defined by a cutoff e.g. 10A :
   >MMalign complex1.pdb complex2.pdb -I 10
    (Distance cutoff is used to determine interface resdiues. Default 8A.)

 5. If you want MM-align to allow cross alignment e.g: Domain swap, Gene Fusion :
   >MMalign complex1.pdb complex2.pdb -DG 

 (First three options,do not change the final structure alignment result)

./MMalign complex1.pdb complex2.pdb

 **************************************************************************
 *                               MM-align                                 *
 *       Aligning protein complex structure by Dynamic Programming        *
 *       Comments on the program, please email to: zhng@umich.edu         *
 **************************************************************************

Protein 1:A793697     Size= 186
Protein 2:B793697     Size= 188 (TM-score is normalized by  188)

Aligned length= 186, RMSD=  0.83, TM-score=0.96781, ID=0.989

 -------- rotation matrix to rotate Chain-1 to Chain-2 ------
 i          t(i)         u(i,1)         u(i,2)         u(i,3)
 1     -7.4207379546  -0.0767574335   0.9970495324  -0.0007254853
 2     -8.4709630656   0.0756837691   0.0065520123   0.9971103441
 3    -12.9232080011   0.9941731557   0.0764807234  -0.0759633823

(":" denotes the residue pairs of distance < 5.0 Angstrom)
t-vwgalghginlnipnfqmtddidevrwergstlvaefkrkpflksgafeilangdlkiknltrddsgtynvtvystngtrildkaldlrileT-VWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE
: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
gtvwgalghginlnipnfqmtddidevrwergstlvaefkrkpflksgafeilangdlkiknltrddsgtynvtvystngtrildkaldlrileGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE

 (Odd no chains of both proteins are in lower case and Even no chains of both proteins are in UPPER case)