Table 2.

Common energy function benchmarking methods

Test	Description	Ref.
Sequence Recovery	Percentage of the native sequence recovered after backbone redesign	[1,51]
Rotamer Recovery	Percentage of native rotamers recovered after full repacking	[51]
ΔΔG Prediction	Prediction of free energy changes upon mutation	[98]
Loop Modeling	Prediction of loop conformations	[99]
High-resolution refinement	Discrimination of native-like decoys upon refinement of ab initio protein models	[100]
Docking	Prediction of protein-protein, protein-peptide, or protein-ligand interfaces	[44,101–103]
Homology Modeling	Structure prediction incorporating homologous information from templates	[104]
Thermodynamic properties	Recapitulation of thermodynamic properties of protein side-chain analogues	[17]
Recapitulation of Xtal structure geometries	Recapitulation of features (e.g. atom-pair distance distribution) from high-resolution protein crystal structures	[50]