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For: Sanchez-garcia R, Macias J, Sorzano C, Carazo J, Segura J. BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction. J Mol Biol 2022. [DOI: 10.1016/j.jmb.2022.167556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 11/20/2022]
Number Cited by Other Article(s)
1
Baeza J, Bedoya M, Cruz P, Ojeda P, Adasme-Carreño F, Cerda O, González W. Main methods and tools for peptide development based on protein-protein interactions (PPIs). Biochem Biophys Res Commun 2025;758:151623. [PMID: 40121967 DOI: 10.1016/j.bbrc.2025.151623] [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: 09/29/2024] [Revised: 03/05/2025] [Accepted: 03/10/2025] [Indexed: 03/25/2025]
2
Xiong D, Qiu Y, Zhao J, Zhou Y, Lee D, Gupta S, Torres M, Lu W, Liang S, Kang JJ, Eng C, Loscalzo J, Cheng F, Yu H. A structurally informed human protein-protein interactome reveals proteome-wide perturbations caused by disease mutations. Nat Biotechnol 2024:10.1038/s41587-024-02428-4. [PMID: 39448882 DOI: 10.1038/s41587-024-02428-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 09/11/2024] [Indexed: 10/26/2024]
3
Alam R, Mahbub S, Bayzid MS. Pair-EGRET: enhancing the prediction of protein-protein interaction sites through graph attention networks and protein language models. Bioinformatics 2024;40:btae588. [PMID: 39360982 PMCID: PMC11495673 DOI: 10.1093/bioinformatics/btae588] [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: 03/04/2024] [Revised: 09/03/2024] [Accepted: 10/01/2024] [Indexed: 10/05/2024]  Open
4
Lin P, Li H, Huang SY. Deep learning in modeling protein complex structures: From contact prediction to end-to-end approaches. Curr Opin Struct Biol 2024;85:102789. [PMID: 38402744 DOI: 10.1016/j.sbi.2024.102789] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
5
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
6
Xiong D, Qiu Y, Zhao J, Zhou Y, Lee D, Gupta S, Torres M, Lu W, Liang S, Kang JJ, Eng C, Loscalzo J, Cheng F, Yu H. Structurally-informed human interactome reveals proteome-wide perturbations by disease mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.24.538110. [PMID: 37162909 PMCID: PMC10168245 DOI: 10.1101/2023.04.24.538110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
7
Michalik I, Kuder KJ. Machine Learning Methods in Protein-Protein Docking. Methods Mol Biol 2024;2780:107-126. [PMID: 38987466 DOI: 10.1007/978-1-0716-3985-6_7] [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: 07/12/2024]
8
Jin Z, Wei Z. Molecular simulation for food protein-ligand interactions: A comprehensive review on principles, current applications, and emerging trends. Compr Rev Food Sci Food Saf 2024;23:e13280. [PMID: 38284571 DOI: 10.1111/1541-4337.13280] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 01/30/2024]
9
Computational Resources for Molecular Biology 2022. J Mol Biol 2022;434:167625. [PMID: 35569508 DOI: 10.1016/j.jmb.2022.167625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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