Web-server for Normal Mode Analysis of proteins

Single Analysis. Calculates the lowest frequency normal modes of your protein and offers different types of calculations to analyse the modes that were calculated.

Comparative Analysis (beta version). Calculates and compares the normal modes of a set of aligned protein structures. This tool is still under development. We will continuously come with upgrades and welcome feedback to help us improve the tool.


Are you submitting large files to WEBnma? Then you might consider entering your email address and we will send you a link that you can visit at a later stage to inspect your results.


Available analyses

Single PDB

  • Deformation energies
  • Eigenvalues
  • Normalized squared atomic displacements
  • Normalized squared fluctuations
  • Interactive mode visualization using JMol: vibrations associated with the lower-frequency modes and vector field representation
  • Overlap between normal modes and a structure difference vector.
  • Correlation matrix of the motions between all the CAlphas of the structure

Comparative

These tools allow the comparative analysis of multiple structures, aligned and uploaded at the PDB format.

  • Deformation Energy profiles
  • Atomic Fluctuation profiles
  • Conformational Overlap Comparison