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For: Yuan Q, Chen J, Zhao H, Zhou Y, Yang Y. Structure-aware protein-protein interaction site prediction using deep graph convolutional network. Bioinformatics 2021;38:125-132. [PMID: 34498061 DOI: 10.1093/bioinformatics/btab643] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/03/2021] [Accepted: 09/03/2021] [Indexed: 02/03/2023]  Open
Number Cited by Other Article(s)
1
Xiao J, Hu G, Zhou X, Zheng Y, Li J. TIDGN: A Transfer Learning Framework for Predicting Interactions of Intrinsically Disordered Proteins with High Conformational Dynamics. J Chem Inf Model 2025;65:4866-4877. [PMID: 40360271 DOI: 10.1021/acs.jcim.5c00422] [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: 05/15/2025]
2
Lai L, Geng J, Duan H, Chen S, Huang L, Yu J. A New Structure Feature Introduced to Predict Protein-Protein Interaction Sites. J Comput Biol 2025;32:520-536. [PMID: 40000026 DOI: 10.1089/cmb.2024.0804] [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: 02/27/2025]  Open
3
Rodrigues CF, de Sousa BL, da Silva JHM, Amorim LAA, Nagano CS, de Oliveira Sousa AR, Carneiro RF, de Oliveira JS, de Freitas CDT, da Silva ALC, Rocha BAM. A novel galectin with triple carbohydrate recognition domain in the parotoid secretion of Rhinella diptycha. Int J Biol Macromol 2025;306:141586. [PMID: 40023411 DOI: 10.1016/j.ijbiomac.2025.141586] [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: 11/10/2024] [Revised: 02/05/2025] [Accepted: 02/26/2025] [Indexed: 03/04/2025]
4
Shao D, Zou Y, Ma L, Yi S. Multiscale and global-local U-Net for protein-protein interaction site prediction. Comput Biol Chem 2025;118:108485. [PMID: 40306099 DOI: 10.1016/j.compbiolchem.2025.108485] [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: 12/13/2024] [Revised: 03/18/2025] [Accepted: 04/21/2025] [Indexed: 05/02/2025]
5
Meng L, Wei L, Wu R. MVGNN-PPIS: A novel multi-view graph neural network for protein-protein interaction sites prediction based on Alphafold3-predicted structures and transfer learning. Int J Biol Macromol 2025;300:140096. [PMID: 39848362 DOI: 10.1016/j.ijbiomac.2025.140096] [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: 11/30/2024] [Revised: 01/04/2025] [Accepted: 01/17/2025] [Indexed: 01/25/2025]
6
Khan S, Noor S, Awan HH, Iqbal S, AlQahtani SA, Dilshad N, Ahmad N. Deep-ProBind: binding protein prediction with transformer-based deep learning model. BMC Bioinformatics 2025;26:88. [PMID: 40121399 PMCID: PMC11929993 DOI: 10.1186/s12859-025-06101-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Accepted: 03/04/2025] [Indexed: 03/25/2025]  Open
7
Li Y, Tian Z, Nan X, Zhang S, Zhou Q, Lu S. HSSPPI: hierarchical and spatial-sequential modeling for PPIs prediction. Brief Bioinform 2025;26:bbaf079. [PMID: 40037640 PMCID: PMC11879409 DOI: 10.1093/bib/bbaf079] [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: 09/23/2024] [Revised: 02/10/2025] [Accepted: 02/13/2025] [Indexed: 03/06/2025]  Open
8
Zhai Z, Xu S, Ma W, Niu N, Qu C, Zong C. LGS-PPIS: A Local-Global Structural Information Aggregation Framework for Predicting Protein-Protein Interaction Sites. Proteins 2025;93:716-727. [PMID: 39520116 DOI: 10.1002/prot.26763] [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: 06/12/2024] [Revised: 10/20/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024]
9
Hui WH, Chen YL, Chang SW. GraphLOGIC: Lethality prediction of osteogenesis imperfecta on type I collagen by a mechanics-informed graph neural network. Int J Biol Macromol 2025;291:139001. [PMID: 39706395 DOI: 10.1016/j.ijbiomac.2024.139001] [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: 09/11/2024] [Revised: 12/16/2024] [Accepted: 12/17/2024] [Indexed: 12/23/2024]
10
Han J, Zhang S, Guan M, Li Q, Gao X, Liu J. GeoNet enables the accurate prediction of protein-ligand binding sites through interpretable geometric deep learning. Structure 2024;32:2435-2448.e5. [PMID: 39488202 DOI: 10.1016/j.str.2024.10.011] [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: 05/17/2024] [Revised: 09/13/2024] [Accepted: 10/08/2024] [Indexed: 11/04/2024]
11
Wang L, Li R, Guan X, Yan S. Prediction of protein interactions between pine and pine wood nematode using deep learning and multi-dimensional feature fusion. FRONTIERS IN PLANT SCIENCE 2024;15:1489116. [PMID: 39687321 PMCID: PMC11646721 DOI: 10.3389/fpls.2024.1489116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Accepted: 11/12/2024] [Indexed: 12/18/2024]
12
Sun X, Wu Z, Su J, Li C. GraphPBSP: Protein binding site prediction based on Graph Attention Network and pre-trained model ProstT5. Int J Biol Macromol 2024;282:136933. [PMID: 39471921 DOI: 10.1016/j.ijbiomac.2024.136933] [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: 09/28/2024] [Revised: 10/21/2024] [Accepted: 10/24/2024] [Indexed: 11/01/2024]
13
Zhou L, Zhu Z, Gao H, Wang C, Khan MA, Ullah M, Khan SU. Multi‐omics graph convolutional networks for digestive system tumour classification and early‐late stage diagnosis. CAAI TRANSACTIONS ON INTELLIGENCE TECHNOLOGY 2024;9:1572-1586. [DOI: 10.1049/cit2.12395] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/05/2024] [Indexed: 01/12/2025]  Open
14
Asediya VS, Anjaria PA, Mathakiya RA, Koringa PG, Nayak JB, Bisht D, Fulmali D, Patel VA, Desai DN. Vaccine development using artificial intelligence and machine learning: A review. Int J Biol Macromol 2024;282:136643. [PMID: 39426778 DOI: 10.1016/j.ijbiomac.2024.136643] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 09/30/2024] [Accepted: 10/15/2024] [Indexed: 10/21/2024]
15
Meng L, Zhang H. GACT-PPIS: Prediction of protein-protein interaction sites based on graph structure and transformer network. Int J Biol Macromol 2024;283:137272. [PMID: 39528184 DOI: 10.1016/j.ijbiomac.2024.137272] [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: 06/28/2024] [Revised: 10/19/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024]
16
Ljubic M, D'Ercole C, Waheed Y, de Marco A, Borišek J, De March M. Computational study of the HLTF ATPase remodeling domain suggests its activity on dsDNA and implications in damage tolerance. J Struct Biol 2024;216:108149. [PMID: 39491691 DOI: 10.1016/j.jsb.2024.108149] [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: 07/19/2024] [Revised: 10/04/2024] [Accepted: 10/28/2024] [Indexed: 11/05/2024]
17
Zhang K, Tao Y, Wang F. AntiBinder: utilizing bidirectional attention and hybrid encoding for precise antibody-antigen interaction prediction. Brief Bioinform 2024;26:bbaf008. [PMID: 39831890 PMCID: PMC11744619 DOI: 10.1093/bib/bbaf008] [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: 07/21/2024] [Revised: 11/07/2024] [Accepted: 01/04/2025] [Indexed: 01/22/2025]  Open
18
Gu M, Yang W, Liu M. Prediction of antibody-antigen interaction based on backbone aware with invariant point attention. BMC Bioinformatics 2024;25:348. [PMID: 39506679 PMCID: PMC11542381 DOI: 10.1186/s12859-024-05961-w] [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: 08/18/2024] [Accepted: 10/16/2024] [Indexed: 11/08/2024]  Open
19
Wang S, Dong K, Liang D, Zhang Y, Li X, Song T. MIPPIS: protein-protein interaction site prediction network with multi-information fusion. BMC Bioinformatics 2024;25:345. [PMID: 39497043 PMCID: PMC11536593 DOI: 10.1186/s12859-024-05964-7] [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: 06/08/2024] [Accepted: 10/21/2024] [Indexed: 11/06/2024]  Open
20
Zhong J, Zhao H, Zhao Q, Zhou R, Zhang L, Guo F, Wang J. RGCNPPIS: A Residual Graph Convolutional Network for Protein-Protein Interaction Site Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:1676-1684. [PMID: 38843057 DOI: 10.1109/tcbb.2024.3410350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
21
Tang T, Li T, Li W, Cao X, Liu Y, Zeng X. Anti-symmetric framework for balanced learning of protein-protein interactions. Bioinformatics 2024;40:btae603. [PMID: 39404784 PMCID: PMC11513017 DOI: 10.1093/bioinformatics/btae603] [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: 07/17/2024] [Revised: 09/13/2024] [Accepted: 10/12/2024] [Indexed: 10/29/2024]  Open
22
González-Avendaño M, López J, Vergara-Jaque A, Cerda O. The power of computational proteomics platforms to decipher protein-protein interactions. Curr Opin Struct Biol 2024;88:102882. [PMID: 39003917 DOI: 10.1016/j.sbi.2024.102882] [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: 03/28/2024] [Revised: 05/31/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024]
23
Zheng Y, Li Q, Freiberger MI, Song H, Hu G, Zhang M, Gu R, Li J. Predicting the Dynamic Interaction of Intrinsically Disordered Proteins. J Chem Inf Model 2024;64:6768-6777. [PMID: 39163306 DOI: 10.1021/acs.jcim.4c00930] [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: 08/22/2024]
24
Ouyang J, Gao Y, Yang Y. PCP-GC-LM: single-sequence-based protein contact prediction using dual graph convolutional neural network and convolutional neural network. BMC Bioinformatics 2024;25:287. [PMID: 39223474 PMCID: PMC11370006 DOI: 10.1186/s12859-024-05914-3] [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: 05/04/2023] [Accepted: 08/22/2024] [Indexed: 09/04/2024]  Open
25
Carroll M, Rosenbaum E, Viswanathan R. Computational Methods to Predict Conformational B-Cell Epitopes. Biomolecules 2024;14:983. [PMID: 39199371 PMCID: PMC11352882 DOI: 10.3390/biom14080983] [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: 07/09/2024] [Revised: 08/04/2024] [Accepted: 08/08/2024] [Indexed: 09/01/2024]  Open
26
Yuan Q, Tian C, Song Y, Ou P, Zhu M, Zhao H, Yang Y. GPSFun: geometry-aware protein sequence function predictions with language models. Nucleic Acids Res 2024;52:W248-W255. [PMID: 38738636 PMCID: PMC11223820 DOI: 10.1093/nar/gkae381] [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: 03/07/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024]  Open
27
Pancino N, Gallegati C, Romagnoli F, Bongini P, Bianchini M. Protein-Protein Interfaces: A Graph Neural Network Approach. Int J Mol Sci 2024;25:5870. [PMID: 38892057 PMCID: PMC11173158 DOI: 10.3390/ijms25115870] [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: 04/14/2024] [Revised: 05/15/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]  Open
28
Rao J, Xie J, Yuan Q, Liu D, Wang Z, Lu Y, Zheng S, Yang Y. A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions. Nat Commun 2024;15:4476. [PMID: 38796523 PMCID: PMC11530528 DOI: 10.1038/s41467-024-48801-4] [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: 12/01/2023] [Accepted: 05/14/2024] [Indexed: 05/28/2024]  Open
29
Yao R, Shen Z, Xu X, Ling G, Xiang R, Song T, Zhai F, Zhai Y. Knowledge mapping of graph neural networks for drug discovery: a bibliometric and visualized analysis. Front Pharmacol 2024;15:1393415. [PMID: 38799167 PMCID: PMC11116974 DOI: 10.3389/fphar.2024.1393415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/12/2024] [Indexed: 05/29/2024]  Open
30
Yuan Q, Tian C, Yang Y. Genome-scale annotation of protein binding sites via language model and geometric deep learning. eLife 2024;13:RP93695. [PMID: 38630609 PMCID: PMC11023698 DOI: 10.7554/elife.93695] [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] [Indexed: 04/19/2024]  Open
31
Wang J, Chen S, Yuan Q, Chen J, Li D, Wang L, Yang Y. Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation. J Comput Chem 2024;45:436-445. [PMID: 37933773 DOI: 10.1002/jcc.27249] [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: 06/26/2023] [Revised: 10/11/2023] [Accepted: 10/21/2023] [Indexed: 11/08/2023]
32
Ashrafzadeh S, Golding GB, Ilie S, Ilie L. Scoring alignments by embedding vector similarity. Brief Bioinform 2024;25:bbae178. [PMID: 38695119 PMCID: PMC11063651 DOI: 10.1093/bib/bbae178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 05/05/2024]  Open
33
Jia P, Zhang F, Wu C, Li M. A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond. Brief Bioinform 2024;25:bbae162. [PMID: 38739759 PMCID: PMC11089422 DOI: 10.1093/bib/bbae162] [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: 01/01/2024] [Revised: 02/17/2024] [Accepted: 03/31/2024] [Indexed: 05/16/2024]  Open
34
Palacios A, Acharya P, Peidl A, Beck M, Blanco E, Mishra A, Bawa-Khalfe T, Pakhrin S. SumoPred-PLM: human SUMOylation and SUMO2/3 sites Prediction using Pre-trained Protein Language Model. NAR Genom Bioinform 2024;6:lqae011. [PMID: 38327870 PMCID: PMC10849187 DOI: 10.1093/nargab/lqae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/17/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]  Open
35
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
36
Zhao C, Wang S. AttCON: With better MSAs and attention mechanism for accurate protein contact map prediction. Comput Biol Med 2024;169:107822. [PMID: 38091726 DOI: 10.1016/j.compbiomed.2023.107822] [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: 10/06/2023] [Revised: 11/19/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024]
37
Fu X, Yuan Y, Qiu H, Suo H, Song Y, Li A, Zhang Y, Xiao C, Li Y, Dou L, Zhang Z, Cui F. AGF-PPIS: A protein-protein interaction site predictor based on an attention mechanism and graph convolutional networks. Methods 2024;222:142-151. [PMID: 38242383 DOI: 10.1016/j.ymeth.2024.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/21/2024]  Open
38
Bravi B. Development and use of machine learning algorithms in vaccine target selection. NPJ Vaccines 2024;9:15. [PMID: 38242890 PMCID: PMC10798987 DOI: 10.1038/s41541-023-00795-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/07/2023] [Indexed: 01/21/2024]  Open
39
Ding H, Li X, Han P, Tian X, Jing F, Wang S, Song T, Fu H, Kang N. MEG-PPIS: a fast protein-protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network. Bioinformatics 2024;40:btae269. [PMID: 38640481 PMCID: PMC11252844 DOI: 10.1093/bioinformatics/btae269] [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: 02/19/2024] [Revised: 03/19/2024] [Accepted: 04/17/2024] [Indexed: 04/21/2024]  Open
40
Zhang S, Han J, Liu J. Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning. Gigascience 2024;13:giae080. [PMID: 39484977 PMCID: PMC11528319 DOI: 10.1093/gigascience/giae080] [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: 07/02/2024] [Revised: 08/29/2024] [Accepted: 09/25/2024] [Indexed: 11/03/2024]  Open
41
Hosseini S, Golding GB, Ilie L. Seq-InSite: sequence supersedes structure for protein interaction site prediction. Bioinformatics 2024;40:btad738. [PMID: 38212995 PMCID: PMC10796176 DOI: 10.1093/bioinformatics/btad738] [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: 05/16/2023] [Revised: 11/17/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024]  Open
42
Zeng X, Meng FF, Li X, Zhong KY, Jiang B, Li Y. GHGPR-PPIS: A graph convolutional network for identifying protein-protein interaction site using heat kernel with Generalized PageRank techniques and edge self-attention feature processing block. Comput Biol Med 2024;168:107683. [PMID: 37984202 DOI: 10.1016/j.compbiomed.2023.107683] [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: 08/21/2023] [Revised: 10/10/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
43
Wu J, Liu B, Zhang J, Wang Z, Li J. DL-PPI: a method on prediction of sequenced protein-protein interaction based on deep learning. BMC Bioinformatics 2023;24:473. [PMID: 38097937 PMCID: PMC10722729 DOI: 10.1186/s12859-023-05594-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]  Open
44
Fang Y, Jiang Y, Wei L, Ma Q, Ren Z, Yuan Q, Wei DQ. DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model. Bioinformatics 2023;39:btad718. [PMID: 38015872 PMCID: PMC10723037 DOI: 10.1093/bioinformatics/btad718] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 11/30/2023]  Open
45
Bi X, Liang W, Zhao Q, Wang J. SSLpheno: a self-supervised learning approach for gene-phenotype association prediction using protein-protein interactions and gene ontology data. Bioinformatics 2023;39:btad662. [PMID: 37941450 PMCID: PMC10666204 DOI: 10.1093/bioinformatics/btad662] [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: 05/15/2023] [Revised: 10/17/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]  Open
46
Kewalramani N, Emili A, Crovella M. State-of-the-art computational methods to predict protein-protein interactions with high accuracy and coverage. Proteomics 2023;23:e2200292. [PMID: 37401192 DOI: 10.1002/pmic.202200292] [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: 04/02/2023] [Revised: 05/24/2023] [Accepted: 06/09/2023] [Indexed: 07/05/2023]
47
Halsana AA, Chakroborty T, Halder AK, Basu S. DensePPI: A Novel Image-Based Deep Learning Method for Prediction of Protein-Protein Interactions. IEEE Trans Nanobioscience 2023;22:904-911. [PMID: 37028059 DOI: 10.1109/tnb.2023.3251192] [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: 03/05/2023]
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Mou M, Pan Z, Zhou Z, Zheng L, Zhang H, Shi S, Li F, Sun X, Zhu F. A Transformer-Based Ensemble Framework for the Prediction of Protein-Protein Interaction Sites. RESEARCH (WASHINGTON, D.C.) 2023;6:0240. [PMID: 37771850 PMCID: PMC10528219 DOI: 10.34133/research.0240] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/08/2023] [Indexed: 09/30/2023]
49
Song Y, Yuan Q, Zhao H, Yang Y. Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures. Brief Bioinform 2023;24:bbad360. [PMID: 37824738 DOI: 10.1093/bib/bbad360] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023]  Open
50
Wu H, Han J, Zhang S, Xin G, Mou C, Liu J. Spatom: a graph neural network for structure-based protein-protein interaction site prediction. Brief Bioinform 2023;24:bbad345. [PMID: 37779247 DOI: 10.1093/bib/bbad345] [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: 07/06/2023] [Revised: 08/22/2023] [Accepted: 09/13/2023] [Indexed: 10/03/2023]  Open
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