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  • Title: A comprehensive review and evaluation of computational methods for identifying protein complexes from protein-protein interaction networks.
    Author: Wu Z, Liao Q, Liu B.
    Journal: Brief Bioinform; 2020 Sep 25; 21(5):1531-1548. PubMed ID: 31631226.
    Abstract:
    Protein complexes are the fundamental units for many cellular processes. Identifying protein complexes accurately is critical for understanding the functions and organizations of cells. With the increment of genome-scale protein-protein interaction (PPI) data for different species, various computational methods focus on identifying protein complexes from PPI networks. In this article, we give a comprehensive and updated review on the state-of-the-art computational methods in the field of protein complex identification, especially focusing on the newly developed approaches. The computational methods are organized into three categories, including cluster-quality-based methods, node-affinity-based methods and ensemble clustering methods. Furthermore, the advantages and disadvantages of different methods are discussed, and then, the performance of 17 state-of-the-art methods is evaluated on two widely used benchmark data sets. Finally, the bottleneck problems and their potential solutions in this important field are discussed.
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