The coils program is based on scoring tables
that are used to compute the probability score
for each segment of a protein sequence (see [1]), and some parameters that
define Gaussian probabilities. Then the main parameters are:
-
the average scoring values of the coiled-coil and globular protein sets;
-
the standard deviation of the scoring values for the
coiled-coil and globular protein sets;
the score for the residue type
in the heptad position
(from 1 to 7).
So that the probability of a coiled-coil segment of length
starting at position
in
a given sequence is computed as
![\begin{displaymath}
Pr_i=\frac{G_{cc}}{G_{cc}+c\cdot G_{g}}
\end{displaymath}](img9.png) |
(1) |
where
is the bias for the most abundant globular class (
) and
and
are defined as
![\begin{displaymath}
G_{cc}=\frac{1}{\surd{2}\sigma_{cc}}e^{-\frac{(x_i-\mu_{cc})^2}{\sigma_{cc}^2}}
\end{displaymath}](img14.png) |
(2) |
![\begin{displaymath}
G_{g}=\frac{1}{\surd{2}\sigma_{g}}e^{-\frac{(x_i-\mu_{g})^2}{\sigma_{g}^2}}
\end{displaymath}](img15.png) |
(3) |
The score
is computed using the matrix
([1]) along the segment
starting
at position
as
![\begin{displaymath}
x_i=(\prod_{h=1}^W f(a_{i+h},h)^{e_h})^{1/N}
\end{displaymath}](img17.png) |
(4) |
where
is the exponential weight of the position
(if not weighted is simply
) and
is the normalization factor
.
The function
is in the case of COILS program is simply
![\begin{displaymath}
f(a_{i+h},h)=S^h(a_{i+h})
\end{displaymath}](img23.png) |
(5) |
where
is the element of the COILS scoring table
accounting for the residue type
in the
heptad position.
Piero Fariselli
2008-04-06