Review of multimer protein–protein interaction complex topology and structure prediction

Protein–protein interactions (PPI) are important for many biological processes. Theoretical understanding of the structurally determining factors of interaction sites will help to understand the underlying mechanism of protein–protein interactions. At the same time, understanding the complex structure of proteins helps to explore their function. And accurately predicting protein complexes from PPI networks helps us understand the relationship between proteins. In the past few decades, scholars have proposed many methods for predicting protein interactions and protein complex structures. In this review, we first briefly introduce the methods and servers for predicting protein interaction sites and interface residue pairs, and then introduce the protein complex structure prediction methods including template-based prediction and template-free prediction. Subsequently, this paper introduces the methods of predicting protein complexes from the PPI network and the method of predicting missing links in the PPI network. Finally, it briefly summarizes the application of machine/deep learning models in protein structure prediction and action site prediction.

Combining Topological Properties and Strong Ties for Link Prediction

Link prediction is an important task that estimates the probability of there being a link between two disconnected nodes. The similarity-based algorithm is a very popular method that employs the node similarities to find links. Most of these types of algorithms focus only on the contribution of common neighborhoods between two nodes. In sociological theory relationships within three degrees are the strong ties that can trigger social behaviors.Thus, strong ties can provide more connection opportunities for unconnected nodes in the networks. As critical topological properties in networks, nodes degrees and node clustering coefficients are well-suited for describing the tightness of connections between nodes. In this paper, we characterize node similarity by utilizing the strong ties of the ego network（i.e., paths within three degrees） and its close connections（node degrees and node clustering coefficients）. We propose a link prediction algorithm that combines topological properties with strong ties, which we called the TPSR algorithm. This algorithm includes TPSR2, TPSR3, and the TPSR4 indices. We evaluate the performance of the proposed algorithm using the metrics of precision and the Area Under the Curve（AUC）. Our experimental results show the TPSR algorithm to perform remarkably better than others.