Table 1.

Summary of terms in the REF15 energy function for proteins.

Term	Description	Weight	Units	Ref.
fa_atr	Attractive energy between two atoms on different residues separated by distance, d	1.0	kcal/mol	[5,6]
fa_rep	Repulsive energy between two atoms on different residues separated by distance, d	0.55	kcal/mol	[5,6]
fa_intra_rep	Repulsive energy between two atoms on the same residue, separated by distance, d	0.005	kcal/mol	[5,6]
fa_sol	Gaussian exclusion implicit solvation energy between protein atoms in different residues	1.0	kcal/mol	[36]
lk_ball_wtd	Orientation-dependent solvation of polar atoms assuming ideal water geometry	1.0	kcal/mol	[50,71]
fa_intra_sol	Gaussian exclusion implicit solvation energy between protein atoms in the same residue	1.0	kcal/mol	[36]
fa_elec	Energy of interaction between two non-bonded charged atoms separated by distance, d	1.0	kcal/mol	[50]
hbond_lr_bb	Energy of short range hydrogen bonds	1.0	kcal/mol	[38,49]
hbond_sr_bb	Energy of long range hydrogen bonds	1.0	kcal/mol	[38,49]
hbond_bb_sc	Energy of backbone-side chain hydrogen bonds	1.0	kcal/mol	[38,49]
hbond_sc	Energy of side chain to side chain hydrogen bonds	1.0	kcal/mol	[38,49]
dslf_fa13	Energy of disulfide bridges	1.25	kcal/mol	[49]
rama_prepro	Probability of backbone ϕ,ψ angles given amino acid type	0.45 kcal/mol/kT	kT	[50,51]
p_aa_pp	Probability of amino acid identity given backbone ϕ,ψ angles	0.4 kcal/mol/kT	kT	[51]
fa_dun	Probability that a chosen rotamer is native-like given backbone ϕ,ψ angles	0.7 kcal/mol/kT	kT	[52]
omega	Backbone-dependent penalty for cis ω dihedrals that deviate from 0° and trans ω dihedrals that deviate from 180°	0.6 kcal/mol/AU	Arbitrary Units (AU)	[72]
pro_close	Penalty for an open proline ring and proline ω bonding energy	1.25 kcal/mol/AU	Arbitrary Units	[51]
yhh_planarity	Sinusoidal penalty for non-planar tyrosine χ3 dihedral angle	0.625 kcal/mol/AU	Arbitrary Units	[49]
ref	Reference energies for amino acid types	1.0 kcal/mol/AU	Arbitrary Units	[1,51]