S1 Text - Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method

A—Distribution of the RMSD within charged (CRG: Arg, Asp, Glu, Hse, Lys, blue); polar (PLR: Asn, Gln, Ser, Thr, Tyr, orange) and other (OTR, green) groups of residues. RMSD was estimated based on the deviation of the last heavy atom in a side chain of the residue in the protein-protein complex and in unbound part. Both protein-protein complex and its each partner were minimized for 5000 steps in NAMD. The inserted graph illustrates the average RMSD of the residues within CRG, PLR and OTR groups for WT (dark grey) and MT (light grey) structures. The analysis was performed for all entries in tDB (see manuscript for details); B–The distribution of the change in RMSD of 1) CRG and PLR residues (orange) and 2) CRG and OTR residues (green) for WT (solid line, open circles) and MT (dash-dot line and solid circles) structures calculated for each case in tDB; Table A—The standardized weights of significant energy terms in predicting the change in binding free energy due to single amino acid substitution; Table B—Variance Inflation Factor calculated based on the Pearson’s correlation coefficient; Table C—Variance Inflation Factor calculated based on the Spearman’s correlation coefficient; Table D—Variance Inflation Factor calculated based on the Kendall’s correlation coefficient.
(DOCX)