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Table 4 The performance of different models on 16 peptides in ModPep16 dataset. All models were subjected to 100 ps molecular dynamics simulations in vacuum environment

From: PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues

   ab initio model PEPstrMOD DSSP model
PDB ID La CA-RMSD B-RMSD CA-RMSD B-RMSD CA-RMSD B-RMSD
 1fevA 15 5.25 5.12 2.20 2.57 1.82 1.78
 1rbdS 15 5.16 5.07 4.86 4.93 5.64 5.08
 1tkqB 15 6.46 5.51 6.11 5.95 5.65 5.46
 1z3lS 15 5.93 5.45 4.28 3.33 4.78 4.65
 1z3mS 15 5.57 5.49 4.81 4.94 3.67 1.73
 1z3pS 15 3.39 3.61 4.16 3.90 6.72 6.62
 2ap8A 20 4.72 4.78 1.37 0.90 1.17 0.91
 2dprA 21 5.60 5.41 1.65 1.52 0.92 0.90
 2fx8P 12 4.17 4.15 4.76 4.77 0.88 0.78
 2k7lB 19 5.99 6.04 6.60 6.44 0.90 0.98
 2rlnS 15 4.16 4.00 6.07 4.69 6.69 2.55
 3cmhA 15 5.21 5.26 4.83 4.75 4.59 4.41
 3kmzC 19 5.32 4.83 1.69 1.24 2.65 2.77
 3zs2D 25 7.23 7.33 5.23 4.85 5.86 5.70
 4lkaB 12 4.65 3.93 4.39 4.17 3.25 2.73
 6cmhA 21 8.81 8.71 5.96 5.80 5.56 3.87
Average   5.48 5.29 4.31 4.05 3.80 3.18
  1. CA-RMSD C-alpha Root Mean Square Deviation, B-RMSD Backbone Root Mean Square Deviation
  2. aLength of the peptide