Structural phylogeny

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Revision as of 02:52, 1 July 2010 (view source) Igchoi (Talk | contribs) (→Concept) ← Older edit		Revision as of 02:59, 1 July 2010 (view source) Igchoi (Talk | contribs) (→Calculation) Newer edit →
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	*[http://scop.berkeley.edu the SCOP DB]		*[http://scop.berkeley.edu the SCOP DB]
	===Torsion angles===		===Torsion angles===
-	====Calculation====	+	====Utilities(calculation)====
-	*MMTB (python toolbox)	+	*[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)
		+
	==Status(result)==		==Status(result)==

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Revision as of 02:59, 1 July 2010

Contents 1 Concept 2 Procedure 2.1 Standard data set 2.2 Torsion angles 2.2.1 Utilities(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

Utilities(calculation)

• MMTK (python molecular modeling toolkit)
• DSSP (by C. Sander)

Status(result)