The LINUS scoring function includes two components: hydrogen-bonding and hydrophobic contacts. 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 and sidechain nitrogens and some side chain oxygens, 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: 3.0 Å <= (N-O distance) <= 4.5 Å; the angle a is 180 ° ± 40; and the angles d' and d are greater than 90 °.

For sidechain donors the definition is more permissive in that we assume free rotation around the donor heavy atom. Only angle d is considered.

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 any carbon atoms in the side chains of hydrophobic residues are juxtaposed. Each carbon atom is assigned an effective contact radius of 2 Å only for the purpose of calculating the hydrophobic contact energy. 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.

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