Mesostate

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Revision as of 16:29, 26 August 2010 (view source) Igchoi (Talk | contribs) (→Mesostate) ← Older edit		Revision as of 16:30, 26 August 2010 (view source) Igchoi (Talk | contribs) (→Status(result)) Newer edit →
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	==Status(result)==		==Status(result)==
-	*TBA	+	*Using [[R]] to check the data
		+	<pre>
		+	# R script
		+	</pre>
		+
	==References==		==References==
	<biblio> #FPP pmid=19188606		<biblio> #FPP pmid=19188606
	</biblio>		</biblio>

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Revision as of 16:30, 26 August 2010

Contents 1 Concept 2 Procedure 2.1 Standard data set 2.2 Torsion angles 2.2.1 Mesostate 2.2.2 Calculation 2.2.3 Alphabet assignment 2.3 Profiling 2.4 Applications 3 Status(result) 4 References

Concept

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...

Mesostate

• Data production by 배형섭
• Torsion angle mesostate by LINUS (Rose Lab)

Calculation

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

Alphabet assignment

• Information theory

Profiling

• Normalization?
• Distance metric?

Applications

Status(result)

• Using R to check the data

# R script

References

1. Error fetching PMID 19188606: [FPP]