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Table 5 The performance of PEPstrMOD on peptides in CyclicPep and ModPep datasets having length in different range. 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

CyclicPep dataset
Length range Peptidesa CA-RMSD Percentb B-RMSD Percentb
 10–15 12 2.99 100 2.60 100
 16–22 12 4.10 66.7 4.06 66.7
 23–30 10 5.31 40 4.95 50
 All (10–30) 34 4.06 70.6 3.81 73.5
ModPep dataset
Length range Peptidesa CA-RMSD Percentb B-RMSD Percentb
 7–10 279 3.16 88.9 2.91 91.4
 11–15 134 4.96 58.2 4.75 61.9
 16–25 88 5.88 51.1 5.44 55.7
 All (7–25) 501 4.12 74.1 3.85 77.2
  1. CA-RMSD C-alpha Root Mean Square Deviation, B-RMSD Backbone Root Mean Square Deviation
  2. aNumber of Peptides
  3. bPercent of peptides with B-RMSD <5 Å