Neighbor Affinity-Based Core-Attachment Method to Detect Protein Complexes in Dynamic PPI Networks
School of Computer Science, Shaanxi Normal University, Xi’an 710119, China
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Molecules 2017, 22(7), 1223; https://doi.org/10.3390/molecules22071223
Received: 28 June 2017
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Revised: 14 July 2017
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Accepted: 18 July 2017
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Published: 24 July 2017
(This article belongs to the Special Issue Computational Analysis for Protein Structure and Interaction)
Protein complexes play significant roles in cellular processes. Identifying protein complexes from protein-protein interaction (PPI) networks is an effective strategy to understand biological processes and cellular functions. A number of methods have recently been proposed to detect protein complexes. However, most of methods predict protein complexes from static PPI networks, and usually overlook the inherent dynamics and topological properties of protein complexes. In this paper, we proposed a novel method, called NABCAM (Neighbor Affinity-Based Core-Attachment Method), to identify protein complexes from dynamic PPI networks. Firstly, the centrality score of every protein is calculated. The proteins with the highest centrality scores are regarded as the seed proteins. Secondly, the seed proteins are expanded to complex cores by calculating the similarity values between the seed proteins and their neighboring proteins. Thirdly, the attachments are appended to their corresponding protein complex cores by comparing the affinity among neighbors inside the core, against that outside the core. Finally, filtering processes are carried out to obtain the final clustering result. The result in the DIP database shows that the NABCAM algorithm can predict protein complexes effectively in comparison with other state-of-the-art methods. Moreover, many protein complexes predicted by our method are biologically significant.
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Keywords:
protein-protein interaction (PPI) network; protein complexes; neighbor affinity; core-attachment
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
MDPI and ACS Style
Lei, X.; Liang, J. Neighbor Affinity-Based Core-Attachment Method to Detect Protein Complexes in Dynamic PPI Networks. Molecules 2017, 22, 1223. https://doi.org/10.3390/molecules22071223
AMA Style
Lei X, Liang J. Neighbor Affinity-Based Core-Attachment Method to Detect Protein Complexes in Dynamic PPI Networks. Molecules. 2017; 22(7):1223. https://doi.org/10.3390/molecules22071223
Chicago/Turabian StyleLei, Xiujuan, and Jing Liang. 2017. "Neighbor Affinity-Based Core-Attachment Method to Detect Protein Complexes in Dynamic PPI Networks" Molecules 22, no. 7: 1223. https://doi.org/10.3390/molecules22071223
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