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. Author manuscript; available in PMC: 2021 May 27.
Published in final edited form as: Annu Rev Biophys. 2020 Oct 16;50:1–30. doi: 10.1146/annurev-biophys-062920-063711

Table 2.

Graph network descriptor consisting of SARS-CoV-2 S-protein RBD, ACE2, and antibodies

Molecule CR3022 B38 CB6 ACE2 BD23 H11-D4 S309 P2B-2F6
PDB ID 6W41 7BZ5 7C01 6M0J 7BYR 6Z43 6WPS 7BWJ
ΔG −15.4 −14.7 −13.5 −11.9 −10.8 −10.3 −9.9 −9.6
R10 335 349 338 279 227 201 256 211
R8 134 138 132 105 106 82 97 82
S10 19.15 30.17 36.56 20.83 10.39 8.91 18.28 17.74
S8 11.69 12.39 13.36 16.60 5.49 4.41 7.04 5.97
d 0.070 0.069 0.072 0.072 0.069 0.077 0.071 0.074
ρ 0.0192 0.0190 0.0196 0.0185 0.0171 0.0190 0.0206 0.0196
〈L〉 13.69 14.26 13.75 13.85 14.80 13.59 13.86 13.98
〈Cb〉 0.0109 0.0111 0.0110 0.0113 0.0130 0.0113 0.0112 0.0117
〈Ce〉 0.052 0.050 0.052 0.051 0.053 0.054 0.054 0.053
〈Cs〉 1590955 2397825 2010826 2105421 813061 2248985 1387110 1562243
〈M〉 847509 1237464 1096771 1132331 413572 1239452 753625 855641
〈Θ〉 0.0192 0.0190 0.0196 0.0185 0.0171 0.0190 0.0206 0.0196

ΔG indicates the predicted binding affinity (kcal/mol) [the predictions are made using the Prodigy web server (87)]; R10 and R8 indicate the FRI with η of 10 and 8, respectively; S10 and S8 indicate the summation of binding affinity changes (ΔΔG kcal/mol) by mutating RBD residues within 10 Å and 8 Å to any Cα of antibodies to glycine; d indicates edge density; ρ indicates degree heterogeneity; 〈L〉 indicates average path length; 〈Cb〉 indicates average betweenness centrality; 〈Ce〉 indicates average eigencentrality; 〈Cs〉 indicates average subgraph centrality; 〈M〉 indicates average communicability; and 〈Θ〉 indicates average communicability angle.

Abbreviations: FRI, flexibility–rigidity index; PDB, Protein Data Bank; RBD, receptor-binding domain; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.