A) PDB Input Selection

Please enter either a single PDB code of interest (see the Help page for more details).

Error: PDB with < 10 or > 600 c-alpha atoms not allowed

B) NMA parameters

Use the drop down menu to change force field. The C-alpha force field is recommended for most applications.

Input Structure Visualization

Input PDB Read Log


Normal mode analysis with Bio3D

This Bio3D WebApp provides a rapid and rigorous tool for normal mode analysis of protein structures. Options include multiple popular elastic network models (ENMs), as well as enhanced analyses including residue fluctuations, mode visualization, dynamic cross-correlations, and overlap analysis.

Start by entering a PDB code of interest then proceed by navigating through following the NEXT buttons.


Residue fluctuations

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Plot options

Plot options



Normal Modes Visualization

Download PDB Trajectory Download PyMOL vector field

Cross correlation analysis

Download PyMOL session Download Plot PDF

Overlap analysis

Press the Launch PDB SEARCH button to enable overlap analysis
Great! Now select a PDB ID from the table below and press the Calculate overlap button

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Plot options

Overlap values

Limited to the first selected structure

Cumulative overlap values


Force fields

calpha: Hinsen, K. et al. (2000) Chemical Physics 261 25-37

anm: Atilgan, A.R. et al. (2001) Biophysical Journal 80 505-515.

sdenm: Dehouck Y. & Mikhailov A.S. (2013) PLoS Comput Biol 9 :e1003209.

reach: Moritsugu K. & Smith J.C. (2008) Biophysical Journal 95 1639-1648.

pfanm: Yang, L. et al. (2009) PNAS 104 .