LDA classification of proteins in the training set.

The results of LDA for the proteins from the training data obtained in the same way as Fig 7 (subset (iii)). (PDF)</p

Comparison of the chain mapping procedure for <i>α</i>-synuclein with and without LDA analysis.

LDA was performed using subset (iii), but in some residues, certain chemical shifts were missing and a reduced dataset was used. The numbers of the spin systems forming the chains are shown in square boxes. The label “pre” stands for the amino acid residue preceding the formed chain. The arrows labeled “LDA” point to the results of the LDA analysis, and the size of the one-letter codes corresponds to the probability as determined by LDA. The arrows labeled “aa-seq filtering” point at the results after amino-acid sequence filtering, reducing the number of possibilities. The arrows pointing left point to unambiguous manual identification of glycine, alanine, serine and threonine (“X” is used for all other amino acid types). All chains for which identification is consistent are shown on both sides, and the correct chain is marked in green. Panels A)-E) correspond to chain-mapping tasks of increasing difficulty (see Section Application 1: Mapping spin-system chains for details).</p

C_<i>β</i>/H_<i>β</i> plane showing the chemical shifts of 17 unfolded proteins from the BMRB (shown in different colors) and 2D projections of higher-dimensional spectra of <i>α</i>-synuclein (shown in black).

Cβ/Hβ plane showing the chemical shifts of 17 unfolded proteins from the BMRB (shown in different colors) and 2D projections of higher-dimensional spectra of α-synuclein (shown in black).</p

Comparison of LDA performance with TSAR amino-acid recognition procedure.

The results were shown for α-synuclein spin sytems. (PDF)</p

Classification accuracy for LDA using H^N, N, CO, C<i>α</i>, C<i>β</i>, H<i>α</i> and H<i>β</i> chemical shifts.

We performed leave-one-out cross-validation with NMR data from the 17 proteins, downloaded from the BMRB. Amino acid distributions are shown as percentages of each type present in each protein.</p

Summary of classification performances.

Values of analyzed classification performance parameters are given for each method. (PDF)</p

Proposed sets of experiments needed to obtain the described chemical shift subsets (i)-(iii).

In subset (iii), 3D HNCO is required for SMFT processing [26].</p

Fig 1 -

The sequential assignment workflow: A) peak picking for all spectra; B) forming spin systems; C) finding sequential links (nuclei whose chemical shifts are used to find the connections between adjacent amino acid residues are marked with different colors); D) forming chains (the numbers of consecutive spin systems are given in boxes; the label “pre” denotes the residue preceding the formed chain for which some chemical shifts are known; E) amino acid recognition based on characteristic chemical shifts; F) chain mapping onto the protein sequence.</p

LDA classification of proteins in the training set.

The results for all 17 proteins from the BMRB that compose the training set are shown, demonstrating the efficiency and accuracy of the LDA approach. (PDF)</p

Application of LDA to the resonance list transfer from BMRB Entry 6968 to the experimental spectrum of <i>α</i>-synuclein.

A) A fragment of the 15N-HSQC spectrum with peaks marked with dots. Peaks from the BMRB list are marked with crosses. Labels indicate the corresponding residue name. B) Correct transfer of assignment from BMRB to the experimental peak list (unambiguous assignments shown with solid arrows, more ambiguous ones—with dashed arrows). The experimental and BMRB peaks corresponding to the successors of the residues of the same amino acid type are marked in the same color. C) Hα, Hβ, Cα and Cβ chemical shifts of the residues preceding the residues shown in panels A) and B). For experimental peaks, these chemical shifts were obtained from the 4D HabCab(CO)NH experiment and then analyzed with LDA, enabling assignment transfer. Color coding as on panel B). The full spectrum with both peak-lists is available at 10.5281/zenodo.7032142.</p