Statistical analysis of representative 60 pairs


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.

The D2 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.

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The D2 code is ... as shown below.

(a) Examples

(a') Examples (detailed information of changes in PHI/PSI dihedral angles)   [Added in 2010-03-27]

(b) Overlap of the variable regions

(c) Average values of five metrics (accuracy, sensitivity, specificity, correlation coeficient, selectivity)

(d) Values of five metrics