The PEPstrMOD server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues. It also handles peptides having various modifications like non-natural residues, terminal modifications (Acetylation/Amidation), Cyclization (N-C, disulfide bridges), conversion of L- to D- amino acids, post translational modifications, etc. The prediction strategy is based on the realization that β-turn is an important and consistent feature of small peptides in addition to regular structures. Thus, the method uses both the regular secondary structure information predicted from PSIPRED and β-turns information predicted from BetaTurns. The structure is further refined with energy minimization and molecular dynamic simulations.
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Kaur, H., Garg, A. and Raghava, G. P. S. (2007)
PEPstr: A de novo method for tertiary structure prediction of small bioactive peptides.
Protein Pept Lett. 14:626-30.
PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues.
Singh S, Singh H, Tuknait A, Chaudhary K, Singh B, Kumaran S, Raghava GP.
Biol Direct. 2015 Dec 21;10:73. doi: 10.1186/s13062-015-0103-4.