Welcome to Peptide Cyclization Module for Structure Modification

This module is used to input an already available peptide tertiary structure in PDB file format. If a structure contains any disulfide cysteine bridge(s), the user can submit the position of cysteine residues to make the S-S bond between those residues. For more information click help

Peptide Structure Submission Form

Peptide structure in PDB format                                                       

Upload a peptide structure in PDB format    
Enter PDB ID              

N-C Cyclization : Yes No     
Cysteine positions with S-S bonds: 

Email Address:

Advanced Options:  

Simulation Time: Peptide Environment:
Download topology files: Cluster Analysis:
Download whole trajectory: Energy and RMS graphs:

If you are using PEPstrMOD, please cite the following articles:
i) Singh, S., Singh, H., Tuknait, A., Chaudhary, K., Singh, B., Kumaran, S. and Raghava, G.P.S. (2015) PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues. Biology Direct 10:73.
ii) 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.
Click Here for PEPstrMOD Manual