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] | |
Depth Index | Sikic [8] | ||
Protrusion | Jones & Thornton [5] | ||
Hydrophobicity | Sikic [8], Ezkurdia [75], RAD-T [37], VORFFIP [40], PresCont [33] | ||
Secondary Structure | |||
Propensity | Conte [64], Zhou & Shan [30], Crowley & Golovin [135], Jones & Thornton [5], Dong [18], Sillerud [136], Levy [137], Tuncbag [58] | ||
Disorder | |||
Curvature | Jones & Thornton [5] | ||
B-Factors | |||
Electrostatic Potential | RAD-T [37] | ||
Side-chain Conformational Entropy | VORFFIP [40] | ||
Residue Contact Frequencies | PredUs [32] | PredUs [32] | PredUs [32] |
Atomic Probability Density Map Features | Chen [7] | Chen [7] | |
Energy of Solvation | Fernandez-Recio method [105], Fiorucci method [9] using APBS [146] |