Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces
Figure 1
Mann-Whitney U-tests for the distributions of numerical attributes around protein surface atoms.
The y-axis of matrix shows the atom type index (i = 30 protein atom types shown in Table 1) and the x-axis shows the j index for the 32 Ai,j features, where j = 1,31 represents the 31 interacting atom types shown in Table 1 and the 32nd feature reflects the local geometry of the protein surface. The matrix element (j,i) shows the Mann-Whitney U-test p-value in color-code for the two groups of Ai,j : one group of Ai,j was calculated for the attribute type j around the surface atom type i in the known PPI sites on proteins in the S432 dataset and the other group was calculated for the same attribute type around the non-PPI site atom type i in the same dataset. The p-values were calculated with the Mann-Whitney U-test implemented as the function ranksum in MATLAB. Two sets of data were input to the function and the output p-value is the probability for the two distributions of data to be statistically indistinguishable. The plus(+) sign in the matrix element indicates that the averaged feature value for the PPI site atoms is larger than the averaged feature value for the non-PPI site atoms and the negative(−) is the opposite. The panel on the right-hand-side of the matrix shows the distributions of protein surface atoms in PPI sites (blue) and non-PPI protein surfaces (red) against protein atom type. The data were derived from proteins in S432.