Structural phylogeny

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Revision as of 02:52, 1 July 2010 (view source) Igchoi (Talk | contribs) (Created page with '==Concept== *Protein structures (3D) were parsed into a finite number of structural alphabets *Using these '''structural alphabets''', identify meaning structural words.. **Frequ…') ← Older edit		Revision as of 02:52, 1 July 2010 (view source) Igchoi (Talk | contribs) (→Concept) Newer edit →
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	*Using these '''structural alphabets''', identify meaning structural words..		*Using these '''structural alphabets''', identify meaning structural words..
	**Frequent structural words (motifs?) and popular sentences (super secondary structures?)		**Frequent structural words (motifs?) and popular sentences (super secondary structures?)
-	*Using '''words'' to relate molecules (proteins) and organismic phylogeny (genomes; book)	+	*Using ''words'' to relate molecules (proteins) and organismic phylogeny (genomes; book)
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	==Procedure==		==Procedure==
	===Standard data set===		===Standard data set===

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Revision as of 02:52, 1 July 2010

Contents 1 Concept 2 Procedure 2.1 Standard data set 2.2 Torsion angles 2.2.1 Calculation 3 Status(result)

Concept

• Protein structures (3D) were parsed into a finite number of structural alphabets
• Using these structural alphabets, identify meaning structural words..
  • Frequent structural words (motifs?) and popular sentences (super secondary structures?)
• Using words to relate molecules (proteins) and organismic phylogeny (genomes; book)

Procedure

Standard data set

• the SCOP DB

Torsion angles

Calculation

• MMTB (python toolbox)
• DSSP (by C. Sander)

Status(result)