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For: Wu Z, Liao Q, Liu B. A comprehensive review and evaluation of computational methods for identifying protein complexes from protein-protein interaction networks. Brief Bioinform 2020;21:1531-1548. [PMID: 31631226 DOI: 10.1093/bib/bbz085] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 01/03/2025]  Open
Number Cited by Other Article(s)
1
Samulevich ML, Carman LE, Aneskievich BJ. Investigating Protein-Protein Interactions of Autophagy-Involved TNIP1. Methods Mol Biol 2025;2879:63-82. [PMID: 38441723 DOI: 10.1007/7651_2024_525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2025]
2
Wu S, Zhang S, Liu CM, Fernie AR, Yan S. Recent Advances in Mass Spectrometry-Based Protein Interactome Studies. Mol Cell Proteomics 2025;24:100887. [PMID: 39608603 PMCID: PMC11745815 DOI: 10.1016/j.mcpro.2024.100887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 11/09/2024] [Accepted: 11/25/2024] [Indexed: 11/30/2024]  Open
3
Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol 2024;31:1665-1687. [PMID: 39303701 DOI: 10.1016/j.chembiol.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
4
Wehrhan L, Keller BG. Prebound State Discovered in the Unbinding Pathway of Fluorinated Variants of the Trypsin-BPTI Complex Using Random Acceleration Molecular Dynamics Simulations. J Chem Inf Model 2024;64:5194-5206. [PMID: 38870039 PMCID: PMC11234359 DOI: 10.1021/acs.jcim.4c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
5
Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E. Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments. Chem Rev 2024;124:3932-3977. [PMID: 38535831 PMCID: PMC11009965 DOI: 10.1021/acs.chemrev.3c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
6
Pan Y, Wang Y, Guan J, Zhou S. PCGAN: a generative approach for protein complex identification from protein interaction networks. Bioinformatics 2023;39:btad473. [PMID: 37531266 PMCID: PMC10457665 DOI: 10.1093/bioinformatics/btad473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 07/23/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023]  Open
7
Dai S, Liu S, Zhou C, Yu F, Zhu G, Zhang W, Deng H, Burlingame A, Yu W, Wang T, Li N. Capturing the hierarchically assorted modules of protein-protein interactions in the organized nucleome. MOLECULAR PLANT 2023;16:930-961. [PMID: 36960533 DOI: 10.1016/j.molp.2023.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/16/2023] [Accepted: 03/21/2023] [Indexed: 05/04/2023]
8
Li B, Altelaar M, van Breukelen B. Identification of Protein Complexes by Integrating Protein Abundance and Interaction Features Using a Deep Learning Strategy. Int J Mol Sci 2023;24:ijms24097884. [PMID: 37175590 PMCID: PMC10178578 DOI: 10.3390/ijms24097884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]  Open
9
Zhan Y, Liu J, Wu M, Tan CSH, Li X, Ou-Yang L. A partially shared joint clustering framework for detecting protein complexes from multiple state-specific signed interaction networks. Comput Biol Med 2023;159:106936. [PMID: 37105110 DOI: 10.1016/j.compbiomed.2023.106936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023]
10
Paquet E, Viktor HL, Madi K, Wu J. Deformable Protein Shape Classification Based on Deep Learning, and the Fractional Fokker-Planck and Kähler-Dirac Equations. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2023;45:391-407. [PMID: 35085073 DOI: 10.1109/tpami.2022.3146796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
11
Manipur I, Giordano M, Piccirillo M, Parashuraman S, Maddalena L. Community Detection in Protein-Protein Interaction Networks and Applications. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:217-237. [PMID: 34951849 DOI: 10.1109/tcbb.2021.3138142] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
12
Lim H, Tsai CJ, Keskin O, Nussinov R, Gursoy A. HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry. Bioinformatics 2022;38:4962-4965. [PMID: 36124958 PMCID: PMC9620825 DOI: 10.1093/bioinformatics/btac633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/05/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]  Open
13
Wang R, Wang C, Ma H. Detecting protein complexes with multiple properties by an adaptive harmony search algorithm. BMC Bioinformatics 2022;23:414. [PMID: 36207692 PMCID: PMC9541083 DOI: 10.1186/s12859-022-04923-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/12/2022] [Indexed: 11/27/2022]  Open
14
Hesami M, Alizadeh M, Jones AMP, Torkamaneh D. Machine learning: its challenges and opportunities in plant system biology. Appl Microbiol Biotechnol 2022;106:3507-3530. [PMID: 35575915 DOI: 10.1007/s00253-022-11963-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/14/2022] [Accepted: 05/07/2022] [Indexed: 12/25/2022]
15
Inference of Molecular Regulatory Systems Using Statistical Path-Consistency Algorithm. ENTROPY 2022;24:e24050693. [PMID: 35626576 PMCID: PMC9142129 DOI: 10.3390/e24050693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]
16
Omranian S, Nikoloski Z, Grimm DG. Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward. Comput Struct Biotechnol J 2022;20:2699-2712. [PMID: 35685359 PMCID: PMC9166428 DOI: 10.1016/j.csbj.2022.05.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 01/05/2023]  Open
17
Rogawski R, Sharon M. Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry. Chem Rev 2022;122:7386-7414. [PMID: 34406752 PMCID: PMC9052418 DOI: 10.1021/acs.chemrev.1c00217] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 01/11/2023]
18
Xiang J, Meng X, Zhao Y, Wu FX, Li M. HyMM: hybrid method for disease-gene prediction by integrating multiscale module structure. Brief Bioinform 2022;23:6547263. [PMID: 35275996 DOI: 10.1093/bib/bbac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/18/2022] [Accepted: 02/13/2022] [Indexed: 11/12/2022]  Open
19
Xiang J, Zhang J, Zhao Y, Wu FX, Li M. Biomedical data, computational methods and tools for evaluating disease-disease associations. Brief Bioinform 2022;23:6522999. [PMID: 35136949 DOI: 10.1093/bib/bbac006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/12/2022]  Open
20
Redhu N, Thakur Z. Network biology and applications. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]  Open
21
Zhou J, Xiong W, Wang Y, Guan J. Protein Function Prediction Based on PPI Networks: Network Reconstruction vs Edge Enrichment. Front Genet 2022;12:758131. [PMID: 34970299 PMCID: PMC8712557 DOI: 10.3389/fgene.2021.758131] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/11/2021] [Indexed: 01/21/2023]  Open
22
Sensitivity of family GH11 Bacillus amyloliquefaciens xylanase A (BaxA) and the T33I mutant to Oryza sativa xylanase inhibitor protein (OsXIP): An experimental and computational study. Enzyme Microb Technol 2022;156:109998. [DOI: 10.1016/j.enzmictec.2022.109998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 11/22/2022]
23
Omranian S, Angeleska A, Nikoloski Z. Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. Comput Struct Biotechnol J 2021;19:5255-5263. [PMID: 34630943 PMCID: PMC8479235 DOI: 10.1016/j.csbj.2021.09.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 12/23/2022]  Open
24
Omranian S, Angeleska A, Nikoloski Z. PC2P: Parameter-free network-based prediction of protein complexes. Bioinformatics 2021;37:73-81. [PMID: 33416831 PMCID: PMC8034538 DOI: 10.1093/bioinformatics/btaa1089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/17/2020] [Accepted: 12/30/2020] [Indexed: 11/12/2022]  Open
25
Li Y, Yao W, Lin J, Gao G, Huang C, Wu Y. Design, synthesis, and biological evaluation of phenyloxadiazole derivatives as potential antifungal agents against phytopathogenic fungi. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-020-02717-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
26
Massoud TF, Paulmurugan R. Molecular Imaging of Protein–Protein Interactions and Protein Folding. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00071-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
27
Wu Z, Liao Q, Fan S, Liu B. idenPC-CAP: Identify protein complexes from weighted RNA-protein heterogeneous interaction networks using co-assemble partner relation. Brief Bioinform 2020;22:6041167. [PMID: 33333549 DOI: 10.1093/bib/bbaa372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/07/2020] [Accepted: 11/20/2020] [Indexed: 12/18/2022]  Open
28
Mazandu GK, Hooper C, Opap K, Makinde F, Nembaware V, Thomford NE, Chimusa ER, Wonkam A, Mulder NJ. IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. Brief Bioinform 2020;22:5943797. [PMID: 33129201 DOI: 10.1093/bib/bbaa277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/12/2020] [Accepted: 09/21/2020] [Indexed: 01/04/2023]  Open
29
Ivanov S, Lagunin A, Filimonov D, Tarasova O. Network-Based Analysis of OMICs Data to Understand the HIV-Host Interaction. Front Microbiol 2020;11:1314. [PMID: 32625189 PMCID: PMC7311653 DOI: 10.3389/fmicb.2020.01314] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022]  Open
30
Liu B, Gao X, Zhang H. BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches. Nucleic Acids Res 2020;47:e127. [PMID: 31504851 PMCID: PMC6847461 DOI: 10.1093/nar/gkz740] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/07/2019] [Accepted: 08/17/2019] [Indexed: 12/14/2022]  Open
31
Wu Z, Liao Q, Liu B. idenPC-MIIP: identify protein complexes from weighted PPI networks using mutual important interacting partner relation. Brief Bioinform 2020;22:1972-1983. [PMID: 32065215 DOI: 10.1093/bib/bbaa016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/15/2020] [Accepted: 01/27/2020] [Indexed: 12/28/2022]  Open
32
Liu B, Zhu Y, Yan K. Fold-LTR-TCP: protein fold recognition based on triadic closure principle. Brief Bioinform 2019;21:2185-2193. [DOI: 10.1093/bib/bbz139] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/01/2019] [Accepted: 10/09/2019] [Indexed: 11/13/2022]  Open
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