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Table 1 Types of peptides that can be handled with different modifications and the resources used to handle such modifications

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

Module name Brief description Resources used
Natural peptides Prediction of peptides having natural residue. PEPstr algorithm using AMBER11.
D-amino acids Incorporation of D amino acids in a peptide. Using inbuilt ‘flip’ command in AMBER11
Terminal modifications Acetylation at N-terminus and/or amidation/N-methylamide group at C-terminus. Using existing force field parameters in AMBER11.
Peptide cyclization N-C cyclization of peptides or peptides having disulfide bridges. Using inbuilt ‘bond’ command in AMBER11.
Non-natural modification Incorporation of any of the 147 non-natural residues. (e.g. Homoserine, N-alkylated residues, β-substituted residues etc.). FFNCAA library comprising 147 non-natural residues compatible with AMBER11.
Incorporation of any of the 210 non-natural residues. (e.g. Ornithine, Norvaline, Halogenated residues etc.). SwissSideChain library comprising 210 non-natural residues compatible with GROMACS.
PTMs of residue Peptides with any of the 32 diverse PTMs. (e.g. phosphorylation, palmitoylation, hydroxylation etc.). FFPTM library compatible with AMBER11.
Advance modification Combination of all the above six modules to provide facility to incorporate multiple modifications in one step. All the resources used in the above modules.
Structure simulations Facility to provide extended simulations. All the resources used in the above modules.