Welcome to Structure Simulations Module for PDB File

The sole purpose of this module is to give an extra facility to the users to simulate their peptide structure. A user needs to input an already available peptide tertiary structure in PDB file format. A user can either paste the peptide coordinates in PDB format or he/she can upload PDB file of his/her peptide. For more information click help

Peptide Structure Submission Form

Paste peptide structure in PDB format       

Upload a peptide structure in PDB format    

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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