Supplementary Material for
VirtualSpectrum, a tool for simulating peak list for multidimensional NMR spectra
Jakob Toudahl Nielsena* and Niels Chr. Nielsena
Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO),
University of Aarhus, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark, Department of
Chemistry
E-mail: ncn@inano.au.dk, jtn@chem.au.dk
a
Contents: Supplementary Figures S1 and S2 and supplementary Table S1
Figure Legends
Figure S1. Visulization of the intensity, fi(d) for a through-space transfer defined in eq. 4 in
Methods, main text, here shown for Fij = 1 and bi = 0 (corresponding to maximum intensity I0
= 1). The intensity is shown as a function of the characteristic distance, rmin, used for
parameterizing the intensity (see Methods, last paragraph). The black, green, red and cyan
curves correspond to the intensity for distance d = 2.5, 3.2, 4.0 and 5.0 Å, respectively. A
reference intensity of 0.1 is shown as a dashes line highlighting the relationship that the
intensity at the characteristic distance: fi(rmin) = 0.1. This implies that if the minimum intensity
threshold (see Methods), hmin is set to hmin = 0.1 a peak corresponding to d = rmin, will be
observed in 50% of the cases, since the intensity is perturbed with random number (eq. 5,
main text), if hmin is set to hmin < 0.1 or hmin > 0.1 the peak will be observed in less than or
more than 50% of the cases, respectively.
Figure S2. Quantitative comparison of observed and simulated spectra. a on the x-axis is
the observed height of the picked peaks in the 20 ms 2D 13C DARR spectrum of Ubiquitin
(Fig. 1 f, main text) and on the y-axis the point intensity at the point of the maximum peak
height in the corresponding simulated spectrum (Fig. 1 c, main text) is shown, the best fit line
for proportionality y = x is shown with a line. b histogram of the chemical shift deviation
between peak positions in the spectra described in a, the deviation was included in the
statistics if a peak in the simulated spectrum was found within a threshold of 0.6 ppm in
experimental spectrum. c same as in a for 2D 1H NOESY of HEWL (Fig. 4, main text), peaks
close to the water signal between 4.54 and 4.84 ppm and close to the diagonal were excluded
from the comparison and only peaks on one side of the diagonal was used in the analysis. d
same as b for the spectra described in c using a threshold for peak shift deviations of 0.05
ppm.
Settings
Line width
(ppb)
fN
Accuracy RMSD
SN
Heavy
Backbone
Precision RMSD
Heavy
Backbone
4
2
75
1.53
0.95
0.81
0.23
6
2
75
1.57
0.96
0.85
0.29
8
2
75
1.45
0.89
0.76
0.19
10
2
75
1.58
1.00
0.82
0.24
12
2
75
1.48
0.90
0.84
0.27
15
2
75
1.49
0.75
0.83
0.27
18
2
75
1.43
0.82
0.87
0.30
20
2
75
1.73
1.10
0.82
0.28
24
2
75
1.61
0.96
0.90
0.39
28
2
75
1.58
1.01
0.95
0.44
32
2
75
2.05
1.38
1.07
0.55
40
2
75
19.90
19.45
9.79
9.22
4
10
25
1.79
1.22
1.08
0.56
6
10
25
1.65
1.09
0.99
0.47
8
10
25
1.53
0.76
1.10
0.60
10
10
25
1.66
1.06
1.03
0.51
12
10
25
1.50
0.81
1.03
0.53
15
10
25
1.62
0.95
1.02
0.53
18
10
25
1.65
0.94
1.04
0.49
20
10
25
1.53
0.80
1.12
0.58
24
10
25
20.83
20.24
8.63
8.29
28
10
25
21.15
20.69
9.02
8.56
32
10
25
21.62
21.11
10.86
10.23
40
10
25
24.30
23.71
12.76
12.20
4
10
75
1.60
1.04
0.77
0.14
12
10
75
1.40
0.82
0.75
0.16
28
10
75
1.62
0.96
0.90
0.39
4
20
75
1.60
0.99
0.77
0.20
12
20
75
1.50
0.91
0.81
0.22
28
20
75
1.51
0.85
0.89
0.35
4
2
10
11.48
10.95
6.94
6.54
12
2
10
8.88
8.38
8.90
8.35
28
2
10
38.77
37.96
17.58
17.03
4
2
25
1.60
0.95
1.49
0.95
12
2
25
1.69
0.98
1.17
0.68
28
2
25
19.45
18.74
8.18
7.87
Table S1: Accuracy and precision RMSDs for Cyana calculation (see legends to Figure 7 in
the main text). The RMSDs are reported for both the heavy atoms and the backbone atoms as
well.