Mesostate
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*Following tools can be used to calculate torsion angles of backbones | *Following tools can be used to calculate torsion angles of backbones | ||
Revision as of 09:59, 5 August 2010
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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...
Mesostate
- Data production by 배형섭
Calculation
- Following tools can be used to calculate torsion angles of backbones
Alphabet assignment
- Information theory
Profiling
- Normalization?
- Distance metric?
Applications
Status(result)
- TBA
