Algorithmic approaches to protein-protein interaction site prediction

Aumentado-Armstrong, Tristan T; Istrate, Bogdan; Murgita, Robert A

doi:10.1186/s13015-015-0033-9

Algorithms for Molecular Biology

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]

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ISSN: 1748-7188

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