Provide a PDB ID or upload a structure file (pdb or mmCIF format) and our server will calculate the 200 lowest-frequency normal modes of the protein structure, followed by the analyses selected with the checkboxes.

The overlap analysis compares the structural difference between two conformations of the same protein to the displacements described by the calculated normal modes of the submitted structure. The structure provided for the overlap analysis must have the same number of CA-atoms as the one the normal modes were calculated for, and the atoms of the two structures should correspond to each other in the order they appear in the PDB-files.

Default alignment

If no alignment at the FASTA format is submitted the default alignment for comparative analyses is performed by MUSTANG. In addition to a FASTA formatted alignment file, you will be able to access the following information:

  • A detailed alignment report including alignment statistics, e.g. similarity or identity ratio
  • RMSD matrix based on multiple superposition, translation vector and rotation matrix for each structure
  • A PDB file containing optimal superposition of all the structures based on the alignment
  • Embedded visualization (based on LiteMol) of the alignment as well as the normal modes

Use your own alignment file

If you use your own alignment file, the alignment file needs to be written in the FASTA format and meet the following requirements:

  • The header line of each sequence should contain the name of the structure file as the first field, (the other fields will not be used by WEBnma)
  • Sequences in the Fasta file and PDB files need to be identical
  • Sequences in the alignment need to be of the same length (including gaps, i.e. "-")
Here is an example:

Size limitation

The size limitation of the submission is 10000 amino acids per structure, for up to 20 structures.

Single Analyses

We show the example of analysis done on the bacterial pentameric proton-gated ion channel (GLIC).

In the overlap analysis, we used the structure in one of the locally-closed states (PDB ID: 3tlu) and open state (PDB ID: 3eam). We first input 3tlu in the PDB ID field of the Single PDB Analyses form, where WEBnm@ will proceed to calculate its normal modes, and then input 3eam in the PDB ID field of Overlap analysis. After the submitted job was finished successfully, we were able to click the link to the analysis result webpage.

The transition from one state to the other is characterized by the following two plots, where the x-axis represents the mode number, and the y-axis represents the dot product of the vectors from the mode and the coordinates of the second structure, and in the case of the cumulative plot, this score sums to one.


In the overlap plot (above), the peaks represent the modes that contribute significantly to this conformational change, the highest of which is the 36th mode. (Note that the first 6 modes represent rigid-body rotational/translational movements, hence 0 score.) The mode index for the given scores are also given in a raw data file. The cumulative overlap (below) shows the number of modes that give the most coverage.

Comparative Analysis

(Input files used: Fasta file Structure 1 Structure 2 Structure 3 Structure 4 )

The single subunits of 3eam, 3tlu were aligned with homologues ELIC (2vl0) and GluCl (3rhw). The following two output plots show respectively the normalized fluctuations profile and the comparative overlap heatmap which uses the Bhattacharya Coefficient (BC) scoring.