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_MIXRANK [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 | |
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. |
FIREDOCK_EI [59] | d | |
FIREDOCK_AB [59] | d | |
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. |
PROPNSTS [67] | i | |
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_SASA [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). |