Structural phylogeny
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==Procedure== | ==Procedure== | ||
===Standard data set=== | ===Standard data set=== | ||
| - | *We are going to use [http://scop.berkeley.edu the SCOP DB]: sequences and structures in the [http://astral.berkeley.edu/ Astral | + | *We are going to use [http://scop.berkeley.edu the SCOP DB]: sequences and structures in the [http://astral.berkeley.edu/ Astral compendium] |
===Torsion angles=== | ===Torsion angles=== | ||
Revision as of 06:46, 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
Status(result)
- TBA
