Structural phylogeny
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==Concept== | ==Concept== | ||
| - | *Protein structures (3D) were parsed into a finite number of structural alphabets | + | *Protein structures (3D) were parsed into a finite number of structural alphabets (e.g. a torsion angle profile) |
| - | *Using these '''structural alphabets''', identify | + | *Using these '''structural alphabets''', we will identify meaningful structural words.. |
**Frequent structural words (motifs?) and popular sentences (super secondary structures?) | **Frequent structural words (motifs?) and popular sentences (super secondary structures?) | ||
| - | *Using ''words'' | + | *Using these''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== | ==Procedure== | ||
Revision as of 06:27, 1 July 2010
Contents |
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
