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Table 9 Criteria used to discriminate the models at 300 K

From: Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

Class Model RMSd mean RMSd fluct. Clusters SSEs Satisfaction score
all-α NS0 + + ++ ++ +++
  ST1 + + ++ ++ +++
  ST2 + + ++ ++ +++
  ST3 + + - + - -
  DT1 + ++ ++ ++ +++
  DT2 - - - ++ ++ +++
all-β NS0 + + ++ + +++
  ST1 + + ++ + +++
  ST2 + + ++ - +++
  DT1b - - - - - - +++
  DT1a + + ++ + +++
  DT2 - + - - - - +++
αβ NS0 + + ++ ++ +++
  ST1 + + ++ ++ +++
  ST2 + + + + - -
  ST3 + + + + - -
  DT1 + + ++ - +++
  DT2 - - + + - +++
  1. RMSd mean, RMSd uctuations, number of clusters along the trajectory, evolution of the secondary structures, hydrophobic and polar satisfaction score. The number of '+' symbolises the confidence in the criterion result. For instance the hydrophobic/polar satisfaction score provides a quantitative answer that is easy to interpret whereas results provided by the RMSd mean are more difficult to judge. The '-' indicates false positives or negatives.