Structural phylogeny
From CSBLwiki
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**[http://dirac.cnrs-orleans.fr/MMTK/ MMTK] (python molecular modeling toolkit) | **[http://dirac.cnrs-orleans.fr/MMTK/ MMTK] (python molecular modeling toolkit) | ||
**[http://swift.cmbi.ru.nl/gv/dssp/ DSSP] (by C. Sander) | **[http://swift.cmbi.ru.nl/gv/dssp/ DSSP] (by C. Sander) | ||
| + | ====Alphabet assignment==== | ||
| + | *Information theory | ||
| + | |||
| + | ===Profiling=== | ||
| + | *Normalization? | ||
| + | *Distance metric? | ||
| + | |||
| + | ===Applications=== | ||
==Status(result)== | ==Status(result)== | ||
*TBA | *TBA | ||
==References== | ==References== | ||
Revision as of 06:50, 1 July 2010
Contents |
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...
Calculation
- Following tools can be used to calculate torsion angles of backbones
Alphabet assignment
- Information theory
Profiling
- Normalization?
- Distance metric?
Applications
Status(result)
- TBA
