From CSBLwiki
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
Torsion angles
images to be posted...
Mesostate
Mesostate - it contains an error
Calculation
- Following tools can be used to calculate torsion angles of backbones
- MMTK (python molecular modeling toolkit)
- DSSP (by C. Sander)
Alphabet assignment
Profiling
- Normalization?
- Distance metric?
Applications
Status(result)
References
Error fetching PMID 19188606:
- Error fetching PMID 19188606: [FPP]