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Table 1 A summary of the scoring functions evaluated

From: The scoring of poses in protein-protein docking: current capabilities and future directions

CP_DECK [72] r The DECK potential, reimplemented based on the original source code.
CP_RMFCA [146] r An α-carbon potential.
CP_RMFCEN1 [147] r A 6 bin distance-dependent centroid-centroid potential.
CP_RMFCEN2 [147] r A 7 bin distance-dependent centroid-centroid potential.
CP_SKOIP [111] r A statistical intermolecular contact potential.
CP_TB [75] r A docking contact potential.
CP_TSC [74] r A 2 bin docking potential.
PAIR [69] p Residue potentials that have been factorised into different energetic contributions (E_pair, E_local, E_ZS3DC, E_3DC and E_3D respectively). These are prefixed with either ‘CP_E’ for energies or ‘CP_Z’ for z-scores, and suffixed with ‘_CB’ for the β-carbon potential and ‘_MIN’ for the minimum inter-residue distance potential. The combination of these into the MixRank ranking strategy is also included. For this method, the 5 largest complexes failed to produce scores and are thus omitted.
LOCAL[69] p
S3DC [69] p
3DC [69] p
3D [69] p
CP_DDGrw [76] r The weighted intermolecular contact potential extracted from ΔΔG data, a preliminary model.
CP_DDGru [76] r The unweighted intermolecular contact potential extracted from ΔΔG data, a preliminary model.
CP_BFVK [148] r A number of residue-level contact potentials which have been used for protein folding studies. For these, the naming scheme and descriptions can be found elsewhere [123, 149]. Contact energy matrices were downloaded from the Potentials’R’Us server.
CP_BL [150] r
CP_BT [151] r
CP_GKS [152] r
CP_HLPL [153] r
CP_MJ1 [154] r
CP_MJ2 [155] r
CP_MJ2h [155] r
CP_MJ3h [114] r
CP_MJPL [153] r
CP_MS [156] r
CP_MSBM [157, 158] r
CP_Qa [159] r
CP_Qm [159] r
CP_Qp [159] r
CP_RO [160] r
CP_SJKG [161] r
CP_SKOa [162] r
CP_SKOb [162] r
CP_TD [163] r
CP_TEl [164] r
CP_TEs [164] r
CP_TS [165] r
CP_VD [166] r
AP_DCOMPLEX [105] r The DComplex potential, reimplementation based on original data file.
AP_dDFIRE [167] d The dDFIRE potential.
AP_DFIRE2 [168] d The DFIRE 2.0 potential.
AP_T1 [74] r The first of two two-step docking potentials.
AP_T2 [74] r The second of two two-step docking potentials.
AP_DOPE [169] r The standard DOPE potential.
AP_DOPE_HR [169] r The high-resolution potentials implemented in MODELLER [170, 171].
AP_ACE [172] d The atomic contact energy desolvation score, calculated using FireDock [59].
AP_OPUS_PSP [113] d The OPUS_PSP folding potential.
AP_GEOMETRIC d The geometric potential reported in Li and Liang: Geometric packing potential function for model selection in protein structure and protein-protein binding predictions, unpublished.
AP_DARS [73] r The DARS decoys-as-reference-state statistical potential.
AP_URS [73] r The URS statistical potential.
AP_MPS [73] r The MFP statistical potential.
AP_WENG [173] r An atomic contact potential.
AP_calRW [174] d The distance-dependent calRW potential.
AP_calRWp [174] d The orientation-dependent calRWplus potential.
AP_GOAP_ALL [175] d The GOAP potential and its two constituent terms.
AP_GOAP_DF [175] d
AP_GOAP_G [175] d
AP_PISA [110] d The PISA score.
AP_DDGrw [76] r The weighted intermolecular contact potential extracted from ΔΔG data.
AP_DDGru [76] r The unweighted intermolecular contact potential extracted from ΔΔG data.
ATTRACT [61] d The ATTRACT scoring function, as calculated in PTools [176].
PYDOCK_TOT [54] i The PyDock scoring function and the electrostatics, van der Waals and desolvation terms it is composed from.
ELE [54] i
VDW [54] i
DESOLV [177] i
FIREDOCK [59] d The general purpose, enzyme-inhibitor and antibody-antigen FireDock scores and the insideness concavity score and hydrogen-bonding, π-π, cation-π and aliphatic potentials they are composed from.
INSIDE [59] d
HBOND [59] d
PI_PI [59] d
CAT_PI [59] d
ALIPH [59] d
SIPPER [67] i The SIPPER score and its amino-acid propensity and desolvation constituents.
ODA [121, 122] i
ZRANK [57] d The original ZRANK scoring function.
ZRANK2 [58] d The reoptimised ZRANK scoring function.
NIP [79] d Interface packing score.
NSC [79] d Surface complementarity score.
ROSETTA [112] d The unweighted Rosetta energy, calculated using PyRosetta.
ROSETTADOCK [112] d The optimised RosettaDock energy, calculated using PyRosetta.
CG_PP [112] d The coarse-grain PyRosetta pair-potential, van der Waals, environment potential and β-potential.
CG_VDW [112] d
CG_ENV [112] d
CG_BETA [112] d
HBOND2 [112] d The atomic-resolution PyRosetta hydrogen bonding potential, amino-acid propensity scores, attractive and repulsive van der Waals energies, pair potential and desolvation energy.
AA_PROP [112] d
FA_ATR [112] d
FA_REP [112] d
PA_PP [112] d
LK_SOLV [178] d
NHB [112] d The total number of hydrogen bonds, calculated using PyRosetta.
CHARMM_TOT [179] d The total CHARMM energy, electrostatic energy, SASA energy and van der Waals, as calculated using the enerCHARMM script in the MMTSB toolset.
CHARMM_ELE [179] d
CHARMM_VDW [179] d
SPIDER [78] d The sub-graph mining based SPIDER score. As the SPIDER program only allowed scoring using a fixed receptor molecule, the unbound receptor conformation was used for this method, with a relaxed parameter set (dRMSD_CutOff = 1.0, intrCvrAbs_CutOff = 20, intrCvrPer_CutOff = 0.3, intrNumPat_CutOff = 10 and intrAveOcc_CutOff = 2).
  1. Shown are the name of the scoring function and reference, how it was calculated (r for reimplemented, d for downloaded, p for personal communication, i for in-house), and a description/notes.