Kevin Reilly
Review of:
Ceroni, Alessio; Frasconi, Paolo; Passerini, Andrea;
and Vullo, Alessandro
Predicting the Disulfide Bonding State of Cysteines
with
Combination of Kernal Machines
Journal of VLSI Signal Processing Systems, 35, 3, (Nov., 2003), 287-295.
Computing Reviews, June 2005, Rev. 0506-0730
PRECIS
See the actual review in Comp. Rev. Here, we overview it.
The review (See CR as cited above) begins with
problem and its importance to assessing structure and ultimately
function of proteins.
The problem has been researched before and this paper points
to previous results and the authors' goals of enriching models.
A Support Vector Machine approach postulates a first stage
to operate as a classifier to separate proteins into three
categories based on whether cysteines appear in all, none,
or some of the disulfide bridges. The second stage employs
a binary classifier to determine individual cysteine states.
The model mathematics and matters such
as simplifying assumptions are laid out carefully.
"Experiments" with SVM models with differing kernel types
(linear, polynomial, and radial bias functions)
are outlined and results (accuracy of 85%)
are presented for five classifiers' performance
on a set of over seven hundred proteins (selection
details presented).
The paper is heavily referenced on the biology and on the
SVM fronts, presenting a probable challenge for readers who
have not been following the topics rather closely.