Table 1.

Statistics of influence of various factors on SPARTA+ chemical shift prediction

	SPARTA	SPARTA+a
		Full	Test I	Test II	Test III	Test IV	Test V
Training Inputb
Residue type	•	•	•	•	•	•	•
φ/ψ/χ1/χ2	•/•/•/×	•/•/•/•	•/•/•/•	•/•/•/•	•/•/•/•	•/•/•/×	•/•/×/×
H-bond	×	•	•	•	×	×	×
S2	×	•	•	×	×	×	×
Training Target δ−δrcc
−δneighbor	•	×	×	×	×	×	×
−δring	•	•	•	•	•	•	•
−δEF	×	•	×	×	×	×	×
Output Δδpred+δrcd
+δneighbor	•	×	×	×	×	×	×
+δring	•	•	•	•	•	•	•
+δEF	×	•	×	×	×	×	×
+ΔHB	•	×	×	×	×	×	×
RMSD(δpred, δobs)e [ppm]
δ15N	2.56 (2.56)	2.45 (2.48)	2.46 (2.48)	2.47 (2.49)	2.52 (2.52)	2.50 (2.51)	2.62 (2.64)
δ1Hα	0.29 (0.27)	0.25 (0.25)	0.27 (0.25)	0.27 (0.25)	0.29 (0.29)	0.29 (0.29)	0.29 (0.29)
δ13C′	1.14 (1.13)	1.09 (1.11)	1.09 (1.11)	1.09 (1.11)	1.13 (1.14)	1.13 (1.14)	1.16 (1.16)
δ13Cα	1.04 (1.01)	0.94 (0.98)	0.94 (0.98)	0.97 (0.99)	0.99 (1.00)	1.02 (1.03)	1.02 (1.05)
δ13Cβ	1.16 (1.06)	1.14 (1.11)	1.14 (1.11)	1.14 (1.11)	1.14 (1.11)	1.15 (1.12)	1.16 (1.14)
δ1HN	0.54 (0.51)	0.49 (0.47)	0.50 (0.48)	0.50 (0.48)	0.58 (0.54)	0.58 (0.54)	0.58 (0.54)

^aSee text (Results and Discussion) for the description of each testing neural network.

^bStructural and dynamic factors used as inputs for the database search (SPARTA) or neural network (SPARTA+) training procedure. All factors are for all three residues of a given tripeptide (see Fig 1A). Parameters included and omitted in each input set are marked • and x, respectively.

^cNMR (secondary) chemical shifts used as the targets (outputs) of the database search (SPARTA) or neural network (SPARTA+) training procedure. The (secondary) NMR chemical shifts were obtained from the difference between the chemical shift δ and the random coil chemical shift δ_rc, after subtracting the corrections from neighboring residues (δ_neighbor), the contributions from ring current effects (δ_ring), or electric fields (δ_EF).

^dOffsets and corrections, in addition to the random coil chemical shift δ_rc, applied to SPARTA or SPARTA+ predicted secondary chemical shift (Δδ^pred), i.e., the final SPARTA/SPARTA+ predicted chemical shifts.

^eRMS deviation between the predicted and experimental (obs) chemical shifts for eleven proteins which are not present in the SPARTA+ training database. For SPARTA+, the prediction performances for the validation datasets (see Methods) in the training database are provided in parentheses. For the SPARTA predictions, performances listed between brackets are those obtained for the 580-protein training database, but with the protein predicted excluded from this database,