Single Protein NMA
Calculate and analyse the lowest frequency normal modes of one protein structure (max. 20 000 amino acids).

Comparative NMA
Calculate and compare the normal modes of a set of aligned protein structures
WEBnm@ will align the uploaded protein structures unless you submit an alignment at the FASTA format
Please provide at least 2 PDB structure files.


Single PDB Analyses

Calculate and analyse the lowest-frequency normal modes of one protein structure

Input your PDB ID

or a structure file

WEBnm@ computes the normal modes

or YOU upload the normal mode file

WEBnm@ performs the calculations

on the server

WEBnm@ shows you the results

on the webpages

Eigenvalues

Compute the eigenvalues for the 200 lowest-frequency modes

Atomic Displacements

Display the displacement of each atom and the atomic fluctuations of the protein

Mode Visualization

Visualize the modes in your browser using LiteMol

Correlation Matrix

Display the correlations between the motions of all the atoms in the protein structure

Overlap

Compare the normal modes of your structure with the transition to a different conformation of the same protein


Upload multiple protein structure files

WEBnm@ computes the alignment and normal modes

for all the structures

WEBnm@ performs the analyses

on the server

WEBnm@ shows you the results

on the webpages

Comparative Analyses

Calculate and compare the normal modes of a set of aligned protein structures

Profile Alignment

Calculate the atomic fluctuations of each protein, and plot them according to the alignment to enable comparison between these proteins

Covariance Similarity

Compare the sets of modes of each protein using BC (Bhattacharyya coefficient) of their covariance matrices and RMSIP (Root Mean Square Inner Product) of the lowest energy modes

If you use WEBnm@ in your research, please do cite the following publication:

Tiwari SP, Fuglebakk E, Hollup SM, Skjærven L, Cragnolini T, Grindhaug SH, Tekle KM, Reuter N. WEBnm@ v2.0: Web server and services for comparing protein flexibility. BMC Bioinformatics. 2014; 15:427

WEBnm@ v. 1.0 was first reported in the following publication:

Hollup SM, Sælensminde G, Reuter N. WEBnm@: a web application for normal mode analysis of proteins BMC Bioinformatics. 2005 Mar 11; 6:52