Please submit a structure file in the pdb format and our server will then calculate the lowest frequency normal modes of your molecule. You will then be offered different types of calculations to analyse the modes that were calculated. Currently, the following analyses are available:

• normalized squared atomic displacements;
• vector field representation of the displacements associated with the lower frequency modes;
• animation of the vibration associated to the first modes (animated gif or dcd trajectory files).
• Deformation and domain analysis; define dynamical domains
• Overlap between normal modes and a structure difference vector
• Mode Visualization in Jmol of the 20 modes with lowest frequency
• Transition Path between two conformations of the same protein (eg. open and closed)

Structure: The structure file should contain only the chain(s) for which you want to calculate normal modes. The server will run computation using all Calphas present in the structure file or the pdb entry.

The server is meant to provide users with simple and automated computation and analysis of low-frequency normal modes for proteins. The computation performed through our server should help the user understand whether his/her protein undergo large amplitude movements, and thus decide if it is worthwile performing a complete study with more thorough analysis. Analysis tools provided here have been described and successfully applied in (Reuter et al., Biophys.J., 2003).

Normal Modes Calculations are performed using the MMTK package (K. Hinsen, J.Comput.Chem., 2000). The force field used is the C-alpha force field (Hinsen et al.,Chem.Phys., 2000). It uses only the Calpha atoms of the protein which are assigned the masses of the whole residue they represent.

Analysis tools available are: deformation energies of each mode, calculation of normalized squared atomic displacements (results are provided for each low frequency mode, either as raw data or as plots with displacement vs. residue number), vector field representation (at the VMD* format), movie representing the vibrations associated with every mode.

* VMD (Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38): http://www.ks.uiuc.edu/Research/vmd