Mechanism of ConSurf
Slide by Eric Martz (2002 - updated 2013)
  1. Obtain amino acid sequence of 3D chain from PDB file specified by user.

  2. Run CSI-BLAST to find the most similar sequences in UNIREF90 (or optionally other sequence databases).
    ConSurf uses sequences with E < 0.0001.
    ConSurfDB filters the sequences to reduce redundancy.

    Enolase (4ENL)

  3. Align sequences with MAFFT (or optionally another algorithm).
    Optionally, user may supply the sequence alignment.

  4. Construct phylogenetic tree from sequence alignment.
    Optionally, user may supply the tree.

  5. Calculate conservation scores (and confidence intervals) for each residue in the 3D chain using a Bayesian method.

  6. Conservation scores are normalized (to mean 0, SD 1) and binned into 9 grades.

  7. Color the 3D model by conservation grades in Proteopedia, FirstGlance in Jmol, PyMol, Chimera, Protein Explorer, or Powerpoint (using the Polyview-3D server). Gallery.
More Details