Table 3

Validation results of our PDZ predictions.

PDZ site in 2H2C

Structure-based nomenclature [53]

Ligand position

Uncertainty coefficient

Distance (Å)

Specificity change


Phe34

β1:β2-7

-3

0.16

15.0

Significant

Ala37

β2-2

-3

0.20

6.4

Significant

Ser39

β2-4

-1

0.16

9.5

Significant

Ser57

β3-4

-3

0.18

7.2

Observed

Asp58

β3-5

-3

0.21

9.1

Observed

Leu60

β3:α1-1

-1

0.24

7.0

Significant


The six sites validated in Tonikian et al. [13] that were not filtered in our calculation are shown, along with their highest-scoring peptide PWM positions. Significant changes of the predicted PWM positions after mutating the PDZ sites were reported for four cases, while in the remaining two cases some changes were also observed.

Yip et al. BMC Biology 2011 9:53   doi:10.1186/1741-7007-9-53

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