BMC Structural Biology

Table 4 Benchmarking correlations between calculated and experimental binding energies using our model and 15 related methods on 100 protein-ligand complexes.

From: Four-body atomic potential for modeling protein-ligand binding affinity: application to enzyme-inhibitor binding energy prediction

Method	Type	Correlation coefficient (r)
Our model	Knowledge-based	0.66
ITScore	Iterative score	0.65
X-Score	Empirical	0.64
DFIRE	Knowledge-based	0.63
DrugScore^CSD	Knowledge-based	0.62
DrugScore^PDB	Knowledge-based	0.60
Cerius2/PLP	Empirical	0.56
SYBYL/G-Score	Force-field-based	0.56
SYBYL/D-Score	Force-field-based	0.48
SYBYL/ChemScore	Empirical	0.47
Cerius2/PMF	Knowledge-based	0.40
DOCK/FF	Force field	0.40
Cerius2/LUDI	Empirical	0.36
Cerius2/Lig-Score	Force-field-based	0.35
SYBYL/F-Score	Empirical	0.30
AutoDock	Force-field-based	0.05

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