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| - | {|align="left" cellpadding="15"
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| - | | __TOC__
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| - | |}
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| - | ==Concept==
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| - | *Protein structures (3D) can be parsed into a finite number of structural alphabets (e.g. a torsion angle of each residue)
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| - | *From these '''structural alphabets''', we will identify meaningful structural words..
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| - | **Frequent structural words (motifs?) and popular sentences (super secondary structures?)
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| - | *Using these structural ''words'', 1) building a profile, 2) relating evolution of molecules (proteins & folds) and organismic phylogeny (genomes; a catalog of words, sentences..)
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| - | *Assumptions - ...
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| - | *Expectation - Multiple Birth (Birth and death) model??
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| - | ==Procedure==
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| - | ===Standard data set===
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| - | *We are going to use [http://scop.berkeley.edu the SCOP DB]: sequences and structures in the [http://astral.berkeley.edu/ Astral compendium]
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| - | ===Torsion angles===
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| - | *Structural alphabets based on torsion angle distributions in the [e:ramachandran plot]
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| - | <pre>
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| - | images to be posted...
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| - | </pre>
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| - | ====Calculation====
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| - | *Following tools can be used to calculate torsion angles of backbones
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| - | **[http://dirac.cnrs-orleans.fr/MMTK/ MMTK] (python molecular modeling toolkit)
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| - | **[http://swift.cmbi.ru.nl/gv/dssp/ DSSP] (by C. Sander)
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| - | ====Alphabet assignment====
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| - | *Information theory
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| - | ===Profiling===
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| - | *Normalization?
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| - | *Distance metric?
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| - | ===Applications===
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| - | ==Status(result)==
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| - | *TBA
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| - | ==References==
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Latest revision as of 03:21, 9 July 2010
