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 Benchmark set: CASP7 high-accuracy structures provided by Cheng
   The PIR MODELLER + PDB template structure can be downloaded in here.
   Because the MCM protocol is not optimal, in the current CHARMM-HM we recommend you to use SA or REX.

Single alignment
Method Modeller SA (Simulated Anneling) REX (Replica Exchage Method) MCM (Monte Carlo Minimization)
Score Tmscore X1 X2 Tmscore X1 X2 Tmscore X1 X2 Tmscore X1 X2
Average 0.85 0.56 0.39 0.85 0.61 0.40 0.82 0.59 0.40 0.47 0.43 0.20

Multi alignment
Method Modeller SA (Simulated Anneling) REX (Replica Exchage Method) MCM (Monte Carlo Minimization)
Score Tmscore X1 X2 Tmscore X1 X2 Tmscore X1 X2 Tmscore X1 X2
Average 0.89 0.57 0.41 0.89 0.62 0.40 0.89 0.61 0.42 0.53 0.43 0.18

   * Individual target result:  1.Single alignment    2. Multiple alignment

 Implementation of Modeller restraint energies into CHARMM.
CA-CA N-O Chi_1 Chi_2 Chi_3 Chi_4 MC-SC SC-SC
Modeller 83.193 97.841 36.892 37.518 33.438 19.360 29.497 44.886 Single templ.
Charmm 83.233 97.902 36.844 37.5135 33.454 19.361 29.514 44.917 Single templ.
Modeller 1134.100 1206.800 33.230 33.484 44.023 18.954 1275.100 553.250 Two templs used
Charmm 1134.160 1206.770 33.263 33.515 44.017 18.953 1275.140 553.268 Two Templs used

 TMscore & Rotamor score of CHARMM-HM Vs. Modeller

 The analytical and numerical forces of all restraint atoms.


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