- Obtain amino acid sequence of 3D chain from PDB file specified by user.
- Run CSI-BLAST to find the most similar sequences in
(or optionally other sequence databases).
ConSurf uses sequences with
E < 0.0001.
the sequences to reduce redundancy.
- Align sequences with
(or optionally another algorithm).
Optionally, user may supply the sequence alignment.
- Construct phylogenetic tree from sequence alignment.
Optionally, user may supply the tree.
- Calculate conservation scores (and confidence intervals)
for each residue in the 3D chain
- Conservation scores are normalized (to mean 0, SD 1)
and binned into 9 grades.
- Color the 3D model by conservation grades
in Proteopedia, FirstGlance in Jmol, PyMol, Chimera, Protein Explorer,
or Powerpoint (using the Polyview-3D server).