Mesostate
From CSBLwiki
(Difference between revisions)
(→References) |
(→Concept) |
||
| Line 3: | Line 3: | ||
|} | |} | ||
==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) |
*From these '''structural alphabets''', we will identify meaningful structural words.. | *From 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 these structural ''words'', 1) building a profile, 2) relating evolution of molecules (proteins & folds) and organismic phylogeny (genomes; a catalog of words, sentences..) | *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 - ... | *Assumptions - ... | ||
| - | *Expectation - Multiple Birth (Birth and death) model?? | + | *Expectation - Multiple Birth (Birth and death) model??--> |
==Procedure== | ==Procedure== | ||
Revision as of 16:26, 26 August 2010
|
Concept
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...
Mesostate
- Data production by 배형섭
- Torsion angle mesostate by LINUS (Rose Lab)
Calculation
- Following tools can be used to calculate torsion angles of backbones
Alphabet assignment
- Information theory
Profiling
- Normalization?
- Distance metric?
Applications
Status(result)
- TBA
References
Error fetching PMID 19188606:
- Error fetching PMID 19188606:
