TY  - JOUR
A1  - Omranian, Sara
A1  - Nikoloski, Zoran
A1  - Grimm, Dominik G.
T1  - Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward
T2  - Computational and structural biotechnology journal
N2  - Physically interacting proteins form macromolecule complexes that drive diverse cellular processes. Advances in experimental techniques that capture interactions between proteins provide us with protein-protein interaction (PPI) networks from several model organisms. These datasets have enabled the prediction and other computational analyses of protein complexes. Here we provide a systematic review of the state-of-the-art algorithms for protein complex prediction from PPI networks proposed in the past two decades. The existing approaches that solve this problem are categorized into three groups, including: cluster-quality-based, node affinity-based, and network embedding-based approaches, and we compare and contrast the advantages and disadvantages. We further include a comparative analysis by computing the performance of eighteen methods based on twelve well-established performance measures on four widely used benchmark protein-protein interaction networks. Finally, the limitations and drawbacks of both, current data and approaches, along with the potential solutions in this field are discussed, with emphasis on the points that pave the way for future research efforts in this field. (c) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).
KW  - Protein Complex Prediction
KW  - Protein-Protein interaction network
KW  - Network
KW  - Clustering Algorithms
KW  - Network embedding
Y1  - 2022
UR  - https://publishup.uni-potsdam.de/frontdoor/index/index/docId/62897
SN  - 2001-0370
VL  - 20
SP  - 2699
EP  - 2712
PB  - Research Network of Computational and Structural Biotechnology (RNCSB)
CY  - Gotenburg
ER  -