Background and Introduction
NMR is a powerful tool for studying protein structure, dynamics, and interaction perturbations. However, the quality of these NMR studies directly depend on the quality of the referencing, since chemical shift values for specific nuclei in proteins are relative to a “reference” value. Often, protein NMR studies are inevitably caught in a “chicken-egg dilemma”—a circle between reference correction and assignment: a correct reference is required for a decent assignment, and a coherent assignment is needed to validate the correct referencing.
Any research in proteins will encounter two type of technologies: NMR (nuclear magnetic resonance) and crystallography. Due to many reasons, NMR is superior in flexibility and convenience. And the data collected from NMR are easy to much intuitive and easy to understand. However as mentioned in the background, NMR has a fundamental issue: it’s need reference before any analysis.
Therefore, to better understand the RefDB data, I made this app that illustrate all the statistics in the dataset.
Simple Histgram
For CA resonance in Helix structure for alanine
A.H.CA <- read.table("~/Dropbox/NMR Referencing/NMRRefCorr/data/Generated-NA/A-H-CA.txt", quote="\"", comment.char="")
library(ggplot2)
plt<-ggplot(data = A.H.CA, aes(x = V1)) + geom_histogram(aes(y=..density..), fill = 'red', binwidth = 0.20, color = I('black')) + stat_function(fun = dnorm, arg = list(mean = mean(A.H.CA$V1, na.rm = T), sd = sd(A.H.CA$V1, na.rm = T)))
suppressWarnings(print(plt))
This figure illustrates the data roughly normal.
Calculated RefDB Statistics for alpha Carbon
## Residue Coil.mu Coil.sd Helix.mu Helix.sd Beta.mu Beta.sd Avg.mu
## 1 Ala 52.840 1.640 54.830 1.05 51.530 1.48 53.44
## 2 Cys(ox) 55.600 2.580 58.000 2.54 54.990 2.00 56.02
## 3 Cys(red) 57.530 3.050 61.310 3.50 56.880 2.02 58.40
## 4 Cys 56.565 2.815 59.655 3.02 55.935 2.01 57.21
## 5 Asp 54.180 1.600 56.700 1.61 53.870 1.64 54.90
## 6 Glu 56.870 1.820 59.110 1.16 55.520 1.67 57.66
## 7 Phe 57.980 2.020 60.810 1.90 56.650 1.59 58.43
## 8 Gly 45.510 1.050 46.910 1.10 45.220 1.17 45.63
## 9 His 55.860 1.960 59.040 1.74 55.090 1.78 56.65
## 10 Ile 61.030 1.900 64.570 1.74 60.050 1.57 61.89
## 11 Lys 56.590 1.780 58.930 1.44 55.400 1.34 57.12
## 12 Leu 54.920 1.700 57.520 1.23 54.080 1.31 55.78
## 13 Met 55.670 1.540 58.090 1.81 54.580 1.24 56.58
## 14 Asn 53.230 1.510 55.450 1.42 52.740 1.47 53.69
## 15 Pro 63.470 1.260 65.490 1.08 62.640 1.03 63.61
## 16 Gln 56.120 1.720 58.470 1.19 54.830 1.41 56.77
## 17 Arg 56.420 1.940 58.930 1.55 55.140 1.64 57.11
## 18 Ser 58.380 1.690 60.880 1.61 57.540 1.40 58.74
## 19 Thr 61.640 2.070 65.610 2.39 61.060 1.59 62.31
## 20 Val 62.060 2.160 66.160 1.55 60.830 1.64 62.82
## 21 Trp 57.780 1.710 60.010 1.77 56.410 1.87 58.05
## 22 Tyr 57.970 2.170 60.980 1.76 56.830 1.71 58.21
## Avg.sd
## 1 1.910
## 2 2.670
## 3 3.320
## 4 2.995
## 5 2.010
## 6 2.090
## 7 2.570
## 8 1.180
## 9 2.440
## 10 2.650
## 11 2.110
## 12 2.060
## 13 2.200
## 14 1.820
## 15 1.460
## 16 2.050
## 17 2.290
## 18 2.010
## 19 2.650
## 20 2.900
## 21 2.340
## 22 2.520
