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Table 6 Cutoff distances (nm), binding constants (molecule −1 s −1), unbinding rate constants (s −1), and σ values for the rule-based model for various resolutions of the native, S-shaped, and U-shaped Pen a 1

From: Extending rule-based methods to model molecular geometry and 3D model resolution

   Model percent reduction
Cfg Value 0 % 25 % 50 % 65 % 75 % 90 % 95 %
N Cutoff 7.0–8.7 5.6–6.2 5.5 5.5 4.0–5.4 4.0–5.4 4.0–5.4
  k f1 1.00 1.00 1.00 1.00 1.00 1.00 1.00
  k f2 6.60e–03 7.58e–03 3.86e–03 4.90e–04 1.27e–03 1.17e–02 1.64e–02
  k r 0.01 0.01 0.01 0.01 0.01 0.01 0.01
  σ 7.03e–04 3.62e–04 6.30e–05 1.62e–03 6.31e–04 1.29e–04 9.25e–04
S Cutoff 6.8–8.3 5.8–6.0 5.8–6.0 5.8–6.0 5.4–5.7 4.5–5.3 4.5–5.3
  k f1 1.00 1.00 1.00 1.00 1.00 1.00 1.00
  k f2 3.56e–03 1.03e–02 8.67e–03 7.84e–03 4.12e–03 6.38e–03 5.58e–03
  k r 0.01 0.01 0.01 0.01 0.01 0.01 0.01
  σ 1.35e–04 1.65e–03 1.48e–04 3.78e–04 9.40e–05 6.77e–04 4.00e–05
U Cutoff 6.8-8.6 6.8–8.6 5.3 5.3 5.3 4.1–5.2 3.9–4.0
  k f1 1.00 1.00 1.00 1.00 1.00 1.00 1.00
  k f2 7.32e-03 1.07e–02 1.94e–03 1.18e–03 1.01e–02 1.04e–02 4.26e–03
  k r 0.01 0.01 0.01 0.01 0.01 0.01 0.01
  σ 4.69e–04 1.41e–03 5.97e–04 2.77e–04 5.23e–04 3.18e–04 2.59e–04