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
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
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
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.