Mesostate
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<pre> | <pre> | ||
# R script | # R script | ||
+ | <pre> | ||
+ | ## load saved R data | ||
+ | load("meso.rdata") | ||
+ | ## analysis | ||
+ | dim(meso) # dimension 11,810,116 residues | ||
+ | meso[1:2,] # check first two rows in the data (list) | ||
+ | dom = unique(meso$Domain) | ||
+ | ndom = length(dom) # 65,485 SCOP domains | ||
+ | nrow(meso)/ndom # average 180 residues (domain size) | ||
+ | # consider 1st, last residues are skipped.. | ||
+ | ## | ||
+ | ## ramachandran plot | ||
+ | ## | ||
+ | # randomly picking 5,000 residue's Phi & Psi | ||
+ | rn = sample(nrow(meso),5000) | ||
+ | png(file="ramachandran.plot") | ||
+ | plot(meso$Phi[rn],meso$Psi[rn],xlab="Phi",ylab="Psi",xlim=c(-180,180),ylim=c(-180,180),main="Ramachandran plot",col="gray") | ||
+ | # randomly picking 5,000 helices | ||
+ | rn = sample(which(meso$Structure=='H'),5000) | ||
+ | points(meso$Phi[rn],meso$Psi[rn],col="green") | ||
+ | # randomly picking 5,000 sheets | ||
+ | rn = sample(which(meso$Structure=='E'),5000) | ||
+ | points(meso$Phi[rn],meso$Psi[rn],col="red") | ||
+ | dev.off() | ||
+ | ## | ||
</pre> | </pre> | ||
*6 x 6 bins | *6 x 6 bins |
Revision as of 09:50, 29 August 2010
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Concept
Procedure
Standard data set
- We are going to use the SCOP DB: sequences and structures in the Astral compendium
Torsion angles
- Structural alphabets based on torsion angle distributions in the ramachandran plot
images to be posted...
Mesostate
- Data production by 배형섭
- Torsion angle mesostate by LINUS (Rose Lab)
Calculation
- Following tools can be used to calculate torsion angles of backbones
Alphabet assignment
- Information theory
Profiling
- Normalization?
- Distance metric?
Applications
Status(result)
- Using R to check the data
# R script <pre> ## load saved R data load("meso.rdata") ## analysis dim(meso) # dimension 11,810,116 residues meso[1:2,] # check first two rows in the data (list) dom = unique(meso$Domain) ndom = length(dom) # 65,485 SCOP domains nrow(meso)/ndom # average 180 residues (domain size) # consider 1st, last residues are skipped.. ## ## ramachandran plot ## # randomly picking 5,000 residue's Phi & Psi rn = sample(nrow(meso),5000) png(file="ramachandran.plot") plot(meso$Phi[rn],meso$Psi[rn],xlab="Phi",ylab="Psi",xlim=c(-180,180),ylim=c(-180,180),main="Ramachandran plot",col="gray") # randomly picking 5,000 helices rn = sample(which(meso$Structure=='H'),5000) points(meso$Phi[rn],meso$Psi[rn],col="green") # randomly picking 5,000 sheets rn = sample(which(meso$Structure=='E'),5000) points(meso$Phi[rn],meso$Psi[rn],col="red") dev.off() ##
- 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
Error fetching PMID 19188606:
- Error fetching PMID 19188606: