Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability

BMC Bioinformatics

Table 2 Predictor variables for the full model

FoldX energy terms (Refer to the online FoldX documentation for descriptions of these terms)
Backbone van der Waals clash Cis bond Disulfide bond Electrostatic Electrostatic Kon	Entropy, main chain Entropy, side chain Helix dipole Hydrogen bond, backbone Hydrogen bond, sidechain Ionization	Solvation, hydrophobic Solvation, polar Torsional clash Total energy Van der Waals Van der Waals clashes
Biochemical properties
Mutation involving proline: 0 or 1 Volume change: absolute difference between van der Waals volumes^a of the wild-type and the substituted amino acids in Å³ Hydrophobicity change: absolute difference between the hydrophobicity indices^b (at pH 7) of the wild-type and the substituted amino acids Charge change: absolute difference between the side chain changes of the wild-type and the substituted amino acids Secondary structure^c: DSSP classification (B, E, G, H, I, S, T, or none) Relative solvent accessibility^d: ranges from 0 (for completely buried) to 1 (completely exposed)

Potential predictors in model search are all \(\mathrm{\Delta \Delta }G\) terms (constituent energies and the total energy) output by FoldX and biochemical properties. The energy terms have standard deviation values that arise from averaging of MD snapshots and are used as predictor variables as well
^aZamyatnin [21]
^bMonera et al. [22]
^cKabsch and Sander [23]
^dTien et al. [24]

ISSN: 1471-2105