Structural phylogeny

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	==Concept==		==Concept==
	*Protein structures (3D) can be parsed into a finite number of structural alphabets (e.g. a torsion angle of each residue)		*Protein structures (3D) can be parsed into a finite number of structural alphabets (e.g. a torsion angle of each residue)

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Revision as of 06:51, 1 July 2010

Contents 1 Concept 2 Procedure 2.1 Standard data set 2.2 Torsion angles 2.2.1 Calculation 2.2.2 Alphabet assignment 2.3 Profiling 2.4 Applications 3 Status(result) 4 References

Concept

• Protein structures (3D) can be parsed into a finite number of structural alphabets (e.g. a torsion angle of each residue)
• From these structural alphabets, we will identify meaningful structural words..
  • Frequent structural words (motifs?) and popular sentences (super secondary structures?)
• Using these structural words, 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)

Alphabet assignment

• Information theory

Profiling

• Normalization?
• Distance metric?

Applications

Status(result)

• TBA

References