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Table 3 The performance of different methods on peptides in CyclicPep 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 PEP-FOLDc PEPstrMODpc
PDB ID La CA-RMSD B-RMSD CA-RMSD B-RMSD CA-RMSD B-RMSD
 1n0c 10 2.98 2.31 2.30 1.83 0.99 0.83
 1n0a 11 3.61 3.92 0.50 0.41 1.09 1.21
 1etl 12 2.07 2.10 3.14 2.47 2.51 2.46
 1im1 12 3.76 3.86 1.85 1.90 2.39 2.44
 1gnb 13 3.45 3.06 5.18 5.13 3.84 3.86
 1hje 13 3.56 3.60 3.64 3.64 3.85 2.47
 1im7 13 4.33 3.51 4.07 3.74 3.73 3.55
 1xgb 13 3.91 3.44 3.59 3.59 2.51 2.62
 2i28 13 3.29 3.23 1.16 0.79 4.66 4.24
 1b45 14 2.93 1.97 3.74 2.17 3.98 2.36
 1jbl 14 4.26 3.36 2.10 2.05 4.01 3.13
 1r8t 15 3.22 2.97 3.84 3.70 2.33 2.08
 1kwd 16 2.24 2.58 2.76 2.18 4.58 4.53
 1mii 16 4.35 4.36 0.86 0.88 2.69 2.46
 2efz 16 5.37 5.27 4.54 3.75 3.40 3.31
 1nim 17 4.35 4.40 3.68 3.53 5.54 5.37
 1ien 19 5.01 4.70 2.54 2.44 2.49 3.46
 1x7k 19 4.79 4.73 5.03 4.92 4.43 4.28
 1kcn 21 4.49 4.41 6.17 5.74 6.58 6.24
 1rpc 21 6.34 6.36 5.86 5.85 6.03 5.96
 1ter 21 7.39 7.26 5.57 5.44 2.56 2.64
 1v6r 21 7.08 7.03 5.91 5.88 5.69 5.85
 1 hp9 22 5.35 5.38 2.76 2.70 2.40 2.03
 2ajw 22 4.88 4.76 0.99 0.83 2.81 2.64
 1oig 24 6.82 6.69 5.56 5.59 6.16 6.14
 1orx 24 7.61 7.41 6.97 6.81 5.85 5.85
 1sp7 24 6.40 6.46 6.47 5.60 5.98 3.80
 2oq9 24 6.28 5.76 9.73 9.56 6.36 5.90
 1wqc 26 6.57 5.03 1.19 1.12 2.10 2.07
 1v5a 28 6.28 6.17 5.06 4.84 3.93 3.76
 1wm8 28 7.78 7.87 6.87 7.07 7.89 7.69
 2it7 28 7.05 7.06 5.59 5.43 4.40 4.25
 2nx7 28 5.65 5.68 6.40 6.31 4.61 4.32
 1mmc 30 7.76 6.01 5.97 5.61 5.80 5.70
Average   5.04 4.78 4.16 3.93 4.06 3.81
  1. PEP-FOLDc: PEP-FOLD predicted peptide structure using cyclic (disulfide bond) constraints
  2. PEPstrMODpc: PEPstrMOD predicted peptide structure using cyclic (disulfide bond) constrains
  3. CA-RMSD C-alpha Root Mean Square Deviation, B-RMSD Backbone Root Mean Square Deviation
  4. aLength of the peptide