Mechanism of ConSurf
Slide by Eric Martz (2002 - 2007)
  1. Obtain amino acid sequence of 3D chain in PDB file specified by user.

  2. Run PSI-BLAST to find the most similar sequences in SWISS-PROT or UniProt.
    By default uses up to 50 sequences with E < 0.001.

    Enolase (4ENL)

  3. Align sequences with MUSCLE (or CLUSTAL-W).
    Optionally, user may supply the sequence alignment.

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

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

  6. Color the 3D model by conservation grades in FirstGlance in Jmol or Protein Explorer. Gallery.