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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

From: Algorithmic approaches to protein-protein interaction site prediction

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]