Empirical force fields for biological macromolecules: Overview and issues

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Evaluation of model refinement in CASP13 (2019, background): “21 Strength-ening these terms has the effect of pushing residues in marginal or disallowed conformations toward the nearest “ favored ” region of Ramachandran space.”
Comparison of multiple Amber force fields and development of improved protein backbone parameters (2006, background): “Dihedral energy parameters in Eq. ( 3 ) corresponding to backbone u/w dihedrals (i.e., Vn and gn) are the adjustable parameters.”
Computational protein structure refinement: Almost there, yet still so far to go (2017, methodology): “111 Back-bone torsion potentials, a key ingredient to correctly reproduce secondary structure propensities, have been ﬁ ne-tuned to balance ab initio data with experimental data on small peptides and torsional distributions in structures from the Protein Data Bank (PDB) 97,107,109 Other…”
Potential energy functions for protein design. (2007, methodology): “Previous reviews have described potential energy functions (PEFs) used for molecular mechanics simulations [1,2], protein design [3,4] and protein structure prediction [5].”