The LINUS scoring function includes three components: hydrogen-bonding, hydrophobic contacts, and a backbone torsion. The hydrogen-bonding and hydrophobic contact scores are calculated between pairs of atoms from residues with a sequence separation between two and N residues, where N is the total number of residues in the polypeptide chain. Sequentially local interactions are considered to be those within a 6-residue interval. A typical LINUS simulation proceeds hierarchically, starting with local interactions and progressing incrementally to 18-residue and N-residue intervals.

1. Hydrogen Bonding Score
In LINUS, hydrogen bond donors are backbone nitrogens, and acceptors are carbonyl oxygens, both backbone and side chain. When identifying hydrogen bonds, both distance and orientation criteria are applied. As diagrammed below, a nitrogen and oxygen are considered to be hydrogen bonded when: 3.5 Å <= (N-O distance) <= 5.0 Å; the angle a is 180 ° ± 40; and the angles d' and d are greater than 90 °.
The score scales linearly with distance, reaching a maximal value at 3.5 Å and decreasing monotonically to zero at 5.0 Å. At the user's option, the hydrogen bond score may be limited to backbone:backbone interactions, backbone:side chain interactions, or both. A maximum score of 0.5 is assigned to backbone:backbone interactions, and a maximum score of 1.0 is assigned to backbone:sidechain interactions. The lower score for the former compensates for the fact that a three-residue move favors hydrogen bond-stabilized α-helical conformers.

2. Hydrophobic Contact Score
Hydrophobic contacts are rewarded when specific atoms in the side chains of hydrophobic residues are juxtaposed. For non-aromatic residues, these atoms are: Ala - CB ; Cys - SG; Ile - CG2; Leu - CD1, CD2; Met - CE; each is assigned an effective contact radius of 2 Å. For the aromatic rings in Phe, Trp and Tyr, the appended pseudo-atom at the ring centroid serves as the contact atom. For two proximate atoms with radii r1 and r2, a maximum score of 1.0 is assigned when the atoms are in contact (i.e. distance between the atom centers <= r1 + r2), and it decreases monotonically to zero at a separation distance equal to the diameter of a water molecule (i.e. distance between the atom centers = r1 + r2 + 2.8 Å.

3. Backbone Torsion Score
Proteins favor conformers on the left side of a Ramachandran plot (φ < 0); α-helix, β-strand, PII and most turn moves have negative φ-values. The most notable exceptions to this trend involve glycine and asparagine residues. Glycines are distributed approximately equally on both sides of the Ramachandran plot, while asparagine residues with φ > 0 are found in about 11 percent of the structural data set. Accordingly, LINUS penalizes moves in which a residue adopts a φ-value by assigning a backbone torsion score of -1.0, except in the cases of glycine, which is rewarded with a positive score of 1.0, and asparagine, which is neither rewarded nor penalized.

The total energy of a conformation used in the Metropolis criterion is given by the negative sum of the three preceding scores: hydrogen bonding, hydrophobic contact and backbone torsion.