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For: Oda T. Improving protein structure prediction with extended sequence similarity searches and deep-learning-based refinement in CASP15. Proteins 2023;91:1712-1723. [PMID: 37485822 DOI: 10.1002/prot.26551] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/25/2023]
Number Cited by Other Article(s)
1
Hameduh T, Miller AD, Heger Z, Haddad Y. The proteomic code: Novel amino acid residue pairing models "encode" protein folding and protein-protein interactions. Comput Biol Med 2025;190:110033. [PMID: 40112562 DOI: 10.1016/j.compbiomed.2025.110033] [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: 08/05/2024] [Revised: 03/11/2025] [Accepted: 03/13/2025] [Indexed: 03/22/2025]
2
Park S, Myung S, Baek M. Advancing protein structure prediction beyond AlphaFold2. Curr Opin Struct Biol 2025;90:102985. [PMID: 39862760 DOI: 10.1016/j.sbi.2025.102985] [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: 10/13/2024] [Revised: 12/31/2024] [Accepted: 01/02/2025] [Indexed: 01/27/2025]
3
Raouraoua N, Lensink MF, Brysbaert G. Massive Sampling Strategy for Antibody-Antigen Targets in CAPRI Round 55 With MassiveFold. Proteins 2025. [PMID: 39868877 DOI: 10.1002/prot.26802] [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: 09/06/2024] [Revised: 12/24/2024] [Accepted: 01/12/2025] [Indexed: 01/28/2025]
4
Lee JW, Won JH, Jeon S, Choo Y, Yeon Y, Oh JS, Kim M, Kim S, Joung I, Jang C, Lee SJ, Kim TH, Jin KH, Song G, Kim ES, Yoo J, Paek E, Noh YK, Joo K. DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function. Bioinformatics 2023;39:btad712. [PMID: 37995286 PMCID: PMC10699847 DOI: 10.1093/bioinformatics/btad712] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023]  Open
5
Huang GJ, Parry TK, McLaughlin WA. Assessment of the Performances of the Protein Modeling Techniques Participating in CASP15 Using a Structure-Based Functional Site Prediction Approach: ResiRole. Bioengineering (Basel) 2023;10:1377. [PMID: 38135968 PMCID: PMC10740689 DOI: 10.3390/bioengineering10121377] [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: 10/17/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]  Open
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