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For: Guo L, He J, Lin P, Huang SY, Wang J. TRScore: a three-dimensional RepVGG-based scoring method for ranking protein docking models. Bioinformatics 2022;38:2444-2451. [PMID: 35199137 DOI: 10.1093/bioinformatics/btac120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/19/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Li H, Nithin C, Kmiecik S, Huang SY. Computational methods for modeling protein-protein interactions in the AI era: Current status and future directions. Drug Discov Today 2025:104382. [PMID: 40398752 DOI: 10.1016/j.drudis.2025.104382] [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: 01/31/2025] [Revised: 04/30/2025] [Accepted: 05/14/2025] [Indexed: 05/23/2025]
2
Grassmann G, Di Rienzo L, Ruocco G, Miotto M, Milanetti E. Compact Assessment of Molecular Surface Complementarities Enhances Neural Network-Aided Prediction of Key Binding Residues. J Chem Inf Model 2025;65:2695-2709. [PMID: 39982412 PMCID: PMC11898074 DOI: 10.1021/acs.jcim.4c02286] [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: 12/06/2024] [Revised: 02/09/2025] [Accepted: 02/13/2025] [Indexed: 02/22/2025]
3
Han B, Zhang Y, Li L, Gong X, Xia K. TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment. Brief Bioinform 2025;26:bbaf083. [PMID: 40062613 PMCID: PMC11891663 DOI: 10.1093/bib/bbaf083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 01/11/2025] [Accepted: 02/17/2025] [Indexed: 05/13/2025]  Open
4
Shirali A, Stebliankin V, Karki U, Shi J, Chapagain P, Narasimhan G. A comprehensive survey of scoring functions for protein docking models. BMC Bioinformatics 2025;26:25. [PMID: 39844036 PMCID: PMC11755896 DOI: 10.1186/s12859-024-05991-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 11/18/2024] [Indexed: 01/24/2025]  Open
5
Shuvo MH, Bhattacharya D. EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks. Comput Struct Biotechnol J 2024;27:160-170. [PMID: 39850657 PMCID: PMC11755013 DOI: 10.1016/j.csbj.2024.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 12/18/2024] [Accepted: 12/20/2024] [Indexed: 01/25/2025]  Open
6
Chen X, Liu J, Park N, Cheng J. A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models. Biomolecules 2024;14:574. [PMID: 38785981 PMCID: PMC11117562 DOI: 10.3390/biom14050574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/07/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]  Open
7
Kim DN, McNaughton AD, Kumar N. Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody-Antigen Interactions. Bioengineering (Basel) 2024;11:185. [PMID: 38391671 PMCID: PMC10886287 DOI: 10.3390/bioengineering11020185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]  Open
8
Zhang L, Wang S, Hou J, Si D, Zhu J, Cao R. ComplexQA: a deep graph learning approach for protein complex structure assessment. Brief Bioinform 2023;24:bbad287. [PMID: 37930021 DOI: 10.1093/bib/bbad287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 11/07/2023]  Open
9
Lee M. Recent Advances in Deep Learning for Protein-Protein Interaction Analysis: A Comprehensive Review. Molecules 2023;28:5169. [PMID: 37446831 DOI: 10.3390/molecules28135169] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023]  Open
10
Shuvo MH, Karim M, Roche R, Bhattacharya D. PIQLE: protein-protein interface quality estimation by deep graph learning of multimeric interaction geometries. BIOINFORMATICS ADVANCES 2023;3:vbad070. [PMID: 37351310 PMCID: PMC10281963 DOI: 10.1093/bioadv/vbad070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/17/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023]
11
Shuvo MH, Karim M, Roche R, Bhattacharya D. PIQLE: protein-protein interface quality estimation by deep graph learning of multimeric interaction geometries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528528. [PMID: 36824789 PMCID: PMC9949034 DOI: 10.1101/2023.02.14.528528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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