Structural phylogeny

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Revision as of 06:28, 1 July 2010

Contents 1 Concept 2 Procedure 2.1 Standard data set 2.2 Torsion angles 2.2.1 Calculation 3 Status(result) 4 References

Concept

• Protein structures (3D) were parsed into a finite number of structural alphabets (e.g. a torsion angle profile)
• Using these structural alphabets, we will identify meaningful structural words..
  • Frequent structural words (motifs?) and popular sentences (super secondary structures?)
• Using thesewords, 1) building a profile, 2) relating evolution of molecules (proteins & folds) and organismic phylogeny (genomes; a catalog of words, sentences..)
• Assumptions...
• Expectation - Multiple Birth (Birth and death) model??

Procedure

Standard data set

• We are going to use the SCOP DB: sequences and structures in the Astral compendium

Torsion angles

• Structural alphabets based on torsion angle distributions in the ramachandran plot

images to be posted...

Calculation

• Following tools can be used to calculate torsion angles of backbones
  • MMTK (python molecular modeling toolkit)
  • DSSP (by C. Sander)

Status(result)

• TBA

References