Table 1.
Summary of four datasets used in this study.
Table 2.
Comparison of the potential predictive capability of different features.
Figure 1.
Distribution comparison of network-based features of heme-binding and non-binding residues.
(a) Degree; (b) Closeness; (c) Betweenness; (d) Clustering Coefficient. For each topological feature, the z-scores of binding and non-binding residues in Dataset 1 are divided into high, medium and low score sections, and then the fraction occupied by each section was calculated.
Figure 2.
Comparison of network-based features of heme-binding and non-binding residues based on residue type.
(a) Degree; (b) Closeness; (c) Betweenness; (d) Clustering Coefficient. For each topological feature, we compared the means of the z-scores of binding and non-binding residues in Dataset 1 for different residue types.
Figure 3.
The ROC curves of different predictors tested on Dataset 1.
Seven SVM-based predictors were built in terms of different feature combination (N/G/C = Network/Geometry/Conservation) and evaluated by a 5-fold cross-validation on Dataset 1.
Table 3.
Performance of different predictors tested on Dataset 1.
Figure 4.
The ROC curves of baseline model and HemeNet tested on Dataset 3.
The baseline model was the predictor considering only conventional features, while HemeNet incorporated network-based features into the baseline model.
Table 4.
Performance of baseline model and HemeNet tested on Dataset 3.
Table 5.
Comparison of network-based features of holo-apo heme protein pairs.
Figure 5.
Visualization of the surface of holo-apo protein pair (2ZDO:A-1XBW:D).
(a) Degree; (b) Closeness; (c) Betweenness; (d) Clustering Coefficient. The color of the surface was changed according to the z-scores of each network-based feature (red/white/yellow = high/medium/low). The heme molecule was shown as a cyan stick. The holo structures (2ZDO:A) were presented in the upper row, and the apo structures (1XBW:D) were presented in the lower row. This figure was produced by PyMOL (www.pymol.org).
Figure 6.
The ROC curves of baseline model and HemeNet tested on Dataset 4.
(a) Holo structures; (b) Apo structures.
Table 6.
Performance of baseline model and HemeNet tested on Dataset 4.
Figure 7.
The ROC curves of ConCavity and HemeNet tested on holo-apo protein pairs.
(a) Holo structures; (b) Apo structures.
Table 7.
Performance comparison of ConCavity and HemeNet.