Structural phylogeny
From CSBLwiki
(Difference between revisions)
(→Concept) |
(→Status(result)) |
||
Line 22: | Line 22: | ||
==Status(result)== | ==Status(result)== | ||
+ | *TBA |
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
Status(result)
- TBA