PURPOSE:
A new encoding approach,
the D2 coding,
has been proposed, but what
for and what its advantages are remains unclear. To demonstrate that
this approach is capable of identifying conformational changes in
proteins, one must 1) use a specifically defined validation dataset, 2)
a well-defined strict testing protocol, and 3) compare his approach to
the existing methods.
METHOD:
The D
2 coding method was
compared to three existing methods: the PB coding [1], the
coding method used by Kuznetsov (and its variation) [2], and the DSSP
coding [3].
[1] de Brevern A.G., Etchebest C. and Hazout S., 2000,
Bayesian probabilistic approach for prediction backbone structures in
terms of protein blocks, Proteins, 41:271-287
[2] Kuznetsov I.B., 2008, Ordered conformational change in the protein
backbone: prediction of conformationally variable positions from
sequence and low-resolution structural data. Proteins, 72(1):74-87.
[3] Kabsh W., Sander C., 1983, Dictionary of protein secondary
structure:
pattern recognition of hydrogen-bonded and geometrical features.
Biopolymers, 22(12):2577-637.
RESULT:
The
D2 code
is ... as shown below.