Supplementary Material for

VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra

Jakob Toudahl Nielsena* and Niels Chr. Nielsena

a 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: ,

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 = ax 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 / Accuracy RMSD / Precision RMSD
Line width (ppb) / fN / SN / Heavy / Backbone / 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.