Map Sequence variability (H)
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onto a 3D structure
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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.
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
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Hits since June/2002
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