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 these modes.

Comparative Analysis. Calculates and compares the normal modes of a set of aligned protein structures.


?
max. 20 000 amino acids
max. 20 structures
max. 10 000 amino acids each

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. Alternatively, you can bookmark the URL appearing in your web browser once you have submitted your job. Results of your submission can be accessed at this URL within two weeks of your submission date.


Available analyses

Single PDB

This section allows the analysis of a single protein structure, with a given PDB ID or upload of a coordinate file in the PDB format.

  • Deformation energies
  • Eigenvalues
  • Normalized squared atomic displacements for the low-frequency modes
  • Normalized squared atomic fluctuations for the protein
  • 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 displaying correlations between the motions of all the Calpha-atoms in the structure

Comparative

This section allows the comparative analysis of multiple structures, aligned and uploaded in the fasta and PDB formats.

  • Deformation energy profiles
  • Normalized squared atomic fluctuation profiles
  • Conformational overlap comparison with Root Mean Squared Inner Product (RMSIP) and Bhattacharyya coefficient (BC) measures.