The scoring metrics from HM and CAD are listed below as they appear left to right (lower is better):
- Score is a summary of the Rosetta energy function, reported in Rosetta Energy Units. When no other specific considerations apply, this is how one should rank models. This score includes entropic and enthalpic components, statistical terms and physical terms. It will not necessarily equal the summation of the other presented terms (minor terms are not displayed).
- Lennard-Jones measures how “well packed” a protein is by using a Lennard-Jones potentials to score atomic attraction and repulsion. A positive score here indicates clashes, implying some problem in the model. A negative score is expected.
- Backbone Torsion quantifies how realistic the backbone angles are, using the Ramachandran plot. As a probabilistic score, this term is expected to be weakly positive.
- Sidechain Torsion quantifies how realistic the sidechain angles are, i.e., how well they fit within the bounds of what we observe in the PDB. Rosetta uses Dunbrack rotamer libraries. As a probabilistic score, this term is expected to be weakly positive.
- Solvation measures how well the model buries hydrophobics and exposes hydrophilic residues, based on the Lazaridis/Karplus implicit model of water around a protein.
- Hydrogen Bond measures how many hydrogen bonds are formed and how well-formed their geometry is, based on PDB-derived statistics. This term is always negative.