Table 3 The protein folding stability changes of 11 missense mutations.

Rank	Mutation	Protein	ΔΔG(kcal/mol)	\({R}_{8}^{w}\)	\({R}_{8}^{m}\)	\(\Delta {\bar{R}}_{8}\)%	\(\langle {C}_{s}^{w}\rangle\)	\(\langle {C}_{s}^{m}\rangle\)	\(\Delta \langle {\bar{C}}_{s}\rangle\)%
Top 1	23403A>G-(D614G)	S protein	0.34	10.27	10.10	1.7	2376	1386	42
Top 2	14408C>T-(P323L)	NSP12(RdRp)	−0.11	9.77	9.87	−1.0	1105	1959	−77
Top 3	25563G>T-(Q57H)	ORF3a	−0.24	11.33	11.66	−1.5	25,061	58,592	−134
Top 4	1059C>T-(T85I)	NSP2	−0.05	12.37	12.51	−1.1	89,764	166,399	−85
Top 5	28881G>A-(R203K)	Nucleocapsid	−1.14	15.69	15.44	1.6	19,356,251	9,436,565	51
Top 6	28883G>C-(G204R)	Nucleocapsid	−1.56	14.99	16.94	13	1,193,960	1,191,199,736	−99,669
Top 7	28882G>A-(R203K)	Nucleocapsid	−1.14	15.69	15.44	1.6	19,356,251	9,436,565	51
Top 8	28144T>C-(L84S)	ORF8	−0.99	12.28	12.05	1.9	12,810	6504	49
Top 9	17858A>G-(Y541C)	NSP13(Helicase)	−0.81	11.52	10.40	9.7	506,640	7271	99
Top 10	17747C>T-(P504L)	NSP13(Helicase)	−0.59	7.52	7.54	0.3	4668	6094	−31
Top 11	27964C>T-(S24L)	ORF8	0.20	11.72	11.66	0.5	11,685	29,777	−155

The folding stability change ΔΔG = ΔG_w − ΔG_m, where ΔG_w and ΔG_m are the folding free energies of the wild type and the mutant type, respectively. \({R}_{8}^{{\mathrm{w}}}\) and \({R}_{8}^{{\mathrm{m}}}\) are FRI rigidities for the wild type and mutant type of the protein with η = 8 Å. Here, \(\langle {C}_{s}^{{\mathrm{w}}}\rangle\) and \(\langle {C}_{s}^{{\mathrm{m}}}\rangle\) are the average subgraph centralities of the wild type and the mutant type, respectively. \(\Delta {\bar{R}}_{8}\) and \(\Delta \langle {\bar{C}}_{s}\rangle\) are the molecular FRI rigidity changes and the average subgraph centrality change.

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