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 Tools    >> H2PDB

Map Sequence variability (H)

onto a 3D structure

This server maps the amino acid variability within a protein sequence alignment onto a 3D structure. Variability is calculated using the Shannon Entropy equation (H), and it is mapped onto the 3D structure via a B factor.

  • The server requires two inputs: 1) a multiple sequence alignment and 2) a PDB file with the 3D-coordinates of one of the sequences in the alignment.

  • Sequence alignment must be in ClustalW format, and must be edited so that it is ungapped with regard to the sequence for which the 3D coordinates are provided.

  • RES numbering in PDB must be consecutive and without missing or repeated RES numbers.

  • IMPORTANT: Alignment and PDB files must be in TEXT format.

  • We suggest that you use our newer version in which you do not need to edit your pdb file.

Your E-mail address:

(if no e-mail address, output will be printed on screen)

Upload Sequence Alignment:

Upload PDB file:


The server returns your input PDB with the sequence variability in the form of a B-factor. Sequence variability can then be visualized using a variety of molecular graphics programs by coloring the molecule by B-factor. Within Rasmol, the most popular program for displaying molecular structures, variability is visualized by simply selecting temperature in the Colours menu.

The color scale for the variability is the following:

where blue is conserved and red is variable


Shannon entropy calculations by Rob Meijers

Graphics and web programming by Pedro Reche

Questinos & Complaints:

Hits since January/2007 Last updated:
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