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. |