Table 3.
Compilation of selected software/methods used to compute features described in Features section, including the predictors utilizing each and the publications describing their utility and recommending their use
| Feature | Software/method | Used by | Recommended by |
|---|---|---|---|
| Accessible Surface Area | PSAIA [117], SurfRace [118], DSSP [119], NACCESS [120], BALL [121], SSpro4 [122], MSMS [123] | Li [29], Sikic [8], Li [38], JET [23], PresCont [33], PredUs [32], Prollo & Meller [39], RAD-T [37] | Chen [16], Jones & Thornton [5], Hoskins [124], Ezkurdia [75] |
| Conservation | HSSP [125,126], ConSurf-HSSP [66], PSI-BLAST [127], Scorecons [128], Rate4Site [129], AL2CO [130] | Li [29], JET [23], BindML [12], RAD-T [37], PresCont [33], VORFFIP [40] | Zhou & Shan [30], RAD-T [37] |
| Depth Index | DPX [131] in PSAIA [117] | Sikic [8], Li [38], VORFFIP [40] | Sikic [8] |
| Protrusion | CX [132] in PSAIA [117] | Sikic [8], Li [38], VORFFIP [40], RAD-T [37], Chen [7] | Jones & Thornton [5] |
| Hydrophobicity | PSAIA [117], QUITE [133], Fauchère & Pliska [134] | Sikic [8], Ezkurdia [75], RAD-T [37], VORFFIP [40], PresCont [33] | Neuvirth [35], Jones & Thornton [5] |
| Secondary Structure | DSSP [119], SSpro4 [122] | Sikic [8], VORFFIP [40], Li [38] | Neuvirth [35], Hoskins [124], Ofran & Rost [22] |
| Propensity | Dong [18], PresCont [33], RAD-T [37] | Dong [18], Jones & Thornton [5], PresCont [33], RAD-T [37] | Conte [64], Zhou & Shan [30], Crowley & Golovin [135], Jones & Thornton [5], Dong [18], Sillerud [136], Levy [137], Tuncbag [58] |
| Disorder | VSL2 [138], RONN [139] | Li [38], RAD-T [37] | Wright [140], Dunker [141], Liu [142], Iakoucheva [143] |
| Curvature | Coleman method [144], SurfRace [118] | Li [38], RAD-T [37], PresCont [33] | Jones & Thornton [5] |
| B-Factors | Curated from PDB [79], Yuan [145] | RAD-T [37], Chung [15], VORFFIP [40], Liu method [54] | Ezkurdia [54,75] |
| Electrostatic Potential | APBS [146], DelPhi [147], FoldX [148,149] | RAD-T [37], Bradford & Westhead [13], Sting-LDA-WNA [42] | RAD-T [37] |
| Side-chain Conformational Entropy | FoldX [148,149] | VORFFIP [40] | Cole & Warwicker [150], Liang [28] |
| Residue Contact Frequencies | PredUs [32] | PredUs [32] | PredUs [32] |
| Atomic Probability Density Map Features | Yu [151], X-SITE [152] | Chen [7] | Chen [7] |
| Energy of Solvation | Fernandez-Recio method [105], Fiorucci method [9] using APBS [146] | Fiorucci [9], RAD-T [37] | Fiorucci [9], RAD-T [37] |