Yhh_planarity A special torsional potential to keep the tyrosine hydroxyl in the plane of the aromatic ring P_aa_pp Probability of amino acid, given torsion values for phi and psiįa_dun Internal energy of sidechain rotamers as derived from Dunbrack's statistics A Harmonic constraint on planarity with standard deviation of ~6 deg. Rama_prepro Ramachandran preferences (with separate lookup tables for pre-proline positions and other positions) Hbond_sc Sidechain-sidechain hydrogen bond energy Hbond_bb_sc Sidechain-backbone hydrogen bond energy
Hbond_lr_bb Backbone-backbone hbonds distant in primary sequence Hbond_sr_bb Backbone-backbone hbonds close in primary sequence Pro_close Proline ring closure energy and energy of psi angle of preceding residue Below is a list of the energy terms used in the ref2015 score function: fa_atr Lennard-Jones attractive between atoms in different residuesįa_rep Lennard-Jones repulsive between atoms in different residuesįa_sol Lazaridis-Karplus solvation energyįa_intra_sol_xover4 Intra-residue Lazaridis-Karplus solvation energyįa_intra_rep Lennard-Jones repulsive between atoms in the same residueįa_elec Coulombic electrostatic potential with a distance-dependent dielectric
Score functions in Rosetta are weighted sums of energy terms, some of which represent physical forces like electrostatics and van der Waals' interactions, while others represent statistical terms like the probability of finding the torsion angles in Ramachandran space. Additionally, you can create a custom score function to suit your requirements. There are also several all-atom score functions for specialized applications on other biomolecules, as well as score functions for the reduced _centroid representation_./full_atom_vs_centroid/fullatom_centroid.md. Rosetta has an optimized energy function or score function called ref2015 for calculating the energy of all atomic interactions in a globular protein made of L-amino acids. In Rosetta, the energy of a biomolecule is calculated by scoring it.
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