Hierarchical representation for PPI sites prediction

Abstract

Background: Protein-protein interactions have pivotal roles in life processes, and aberrant interactions are associated with various disorders. Interaction site identification is key for understanding disease mechanisms and design new drugs. Effective and efficient computational methods for the PPI prediction are of great value due to the overall cost of experimental methods. Promising results have been obtained using machine learning methods and deep learning techniques, but their effectiveness depends on protein representation and feature selection.

Results: We define a new abstraction of the protein structure, called hierarchical representations, considering and quantifying spatial and sequential neighboring among amino acids. We also investigate the effect of molecular abstractions using the Graph Convolutional Networks technique to classify amino acids as interface and no-interface ones. Our study takes into account three abstractions, hierarchical representations, contact map, and the residue sequence, and considers the eight functional classes of proteins extracted from the Protein-Protein Docking Benchmark 5.0. The performance of our method, evaluated using standard metrics, is compared to the ones obtained with some state-of-the-art protein interface predictors. The analysis of the performance values shows that our method outperforms the considered competitors when the considered molecules are structurally similar.

Conclusions: The hierarchical representation can capture the structural properties that promote the interactions and can be used to represent proteins with unknown structures by codifying only their sequential neighboring. Analyzing the results, we conclude that classes should be arranged according to their architectures rather than functions.

Keywords: Graph convolutional networks; Hierarchical representation; Protein–protein interaction.

Fig. 1

Adjacency graph construction for a given set of proteins

Fig. 2

PPI interface residue classification with a semi-supervised GCN framework

Fig. 3

Average Receiver Operating Characteristic curve comparison of the proposed PPI interface prediction method by using hierarchical representation, contact map and sequence as protein representation with different thresholds (6Å, 8Å, 10Å, 12Å) for each protein class

Fig. 4

Average Precision-Recall curve comparison of the proposed PPI interface prediction method by using hierarchical representation, contact map and sequence as protein representation with different thresholds (6Å, 8Å, 10Å, 12Å) for each protein class