Mesostate

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Revision as of 16:30, 26 August 2010 (view source) Igchoi (Talk | contribs) (→Status(result)) ← Older edit		Revision as of 01:50, 28 August 2010 (view source) Igchoi (Talk | contribs) (→Status(result)) Newer edit →
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	<pre>		<pre>
	# R script		# R script
		+	</pre>
		+	*6 x 6 bins
		+	<pre>
		+	> print(bins)
		+	[,1]  [,2]    [,3]  [,4]  [,5]    [,6]
		+	[1,]  90545 18116  83067 120228 284531 1369188
		+	[2,] 100305 84717 3685965 485872 653175 2066098
		+	[3,]  4849 86683 1565006  5826  39358  294463
		+	[4,]  23516  9348    2594 135671  25882    3456
		+	[5,]  54491 12777  109935 234363  17244  41903
		+	[6,]  35495  3524  13284  6641  5944  34984
	</pre>		</pre>

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Revision as of 01:50, 28 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

• 6 x 6 bins

> print(bins)
       [,1]  [,2]    [,3]   [,4]   [,5]    [,6]
[1,]  90545 18116   83067 120228 284531 1369188
[2,] 100305 84717 3685965 485872 653175 2066098
[3,]   4849 86683 1565006   5826  39358  294463
[4,]  23516  9348    2594 135671  25882    3456
[5,]  54491 12777  109935 234363  17244   41903
[6,]  35495  3524   13284   6641   5944   34984

References

1. Error fetching PMID 19188606: [FPP]