For sake of clarity we have to mention that this is our implementation of PCOILS, and we cannot
guarantee that the original PCOILS program works in the same way, since the authors
does not show the explicit algorithm [2]. However, in case of our PCOILS, all the
machinery described above still remains untouched, with the exception of function
(Eq. 5). Since we are dealing with evolutionary information
computed from a given multiple alignment, instead of the single-sequence
we work with the profile , that represents the frequency of residue in position of
the alignment.
In this case the PCOILS score is still defined by an equation similar to Eq.4,
but with the new function: