Computer simulations of protein models on lattices
have been widely used as an aid in the study of protein
folding process. Following the suggestion of Raghunathan
and Jernigan (1997, Protein Sci 6:2072–2083)
that the cubo-octahedral lattice can allow a more realistic
representation of proteins than other lattices, we propose
here the use of a new set of internal coordinates θ
for the description of a protein model on this lattice.
An easy procedure for the conversion of the θ coordinates
to the Cartesian coordinates is also described. When the
Contact Interaction approach, already proposed by us for
simulations on square or cubic lattices, was applied to
the cubo-octahedral lattice, the system obeyed the correct
thermodynamics derived from the definition of energy. Thus,
lattice simulations of protein models, in which secondary
structure elements such as α-helices or β-strands
can be easily identifiable, can be performed.