Structural phylogeny

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Revision as of 03:01, 1 July 2010 (view source) Igchoi (Talk | contribs) (→Standard data set) ← Older edit		Revision as of 03:02, 1 July 2010 (view source) Igchoi (Talk | contribs) (→Utilities(calculation)) Newer edit →
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	===Torsion angles===		===Torsion angles===
-	====Utilities(calculation)====	+	====Calculation====
-	*[http://dirac.cnrs-orleans.fr/MMTK/ MMTK] (python molecular modeling toolkit)	+	*Following tools can be used to calculate torsion angles of backbones
-	*[http://swift.cmbi.ru.nl/gv/dssp/ DSSP] (by C. Sander)	+	**[http://dirac.cnrs-orleans.fr/MMTK/ MMTK] (python molecular modeling toolkit)
		+	**[http://swift.cmbi.ru.nl/gv/dssp/ DSSP] (by C. Sander)
	==Status(result)==		==Status(result)==

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Revision as of 03:02, 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

• We are going to use the SCOP DB: sequences and structures in the Astral compendium

Torsion angles

Calculation

• Following tools can be used to calculate torsion angles of backbones
  • MMTK (python molecular modeling toolkit)
  • DSSP (by C. Sander)

Status(result)