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For: Mikhaylov V, Brambley CA, Keller GLJ, Arbuiso AG, Weiss LI, Baker BM, Levine AJ. Accurate modeling of peptide-MHC structures with AlphaFold. Structure 2024;32:228-241.e4. [PMID: 38113889 PMCID: PMC10872456 DOI: 10.1016/j.str.2023.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/17/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023]
Number Cited by Other Article(s)
1
Huang XY, Zhang X, Xing L, Huang SX, Zhang C, Hu XC, Liu CG. Promoting lignocellulosic biorefinery by machine learning: progress, perspectives and challenges. BIORESOURCE TECHNOLOGY 2025;428:132434. [PMID: 40139471 DOI: 10.1016/j.biortech.2025.132434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 02/28/2025] [Accepted: 03/19/2025] [Indexed: 03/29/2025]
2
Pandey A, Lenin RR, Patiyal S, Agrawal P. High Throughput Meta-analysis of Antimicrobial Peptides for Characterizing Class Specific Therapeutic Candidates: An In Silico Approach. Probiotics Antimicrob Proteins 2025:10.1007/s12602-025-10596-1. [PMID: 40423878 DOI: 10.1007/s12602-025-10596-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2025] [Indexed: 05/28/2025]
3
Najar Najafi N, Karbassian R, Hajihassani H, Azimzadeh Irani M. Unveiling the influence of fastest nobel prize winner discovery: alphafold's algorithmic intelligence in medical sciences. J Mol Model 2025;31:163. [PMID: 40387957 DOI: 10.1007/s00894-025-06392-x] [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: 12/01/2024] [Accepted: 05/06/2025] [Indexed: 05/20/2025]
4
Naffaa MM, Al-Ewaidat OA, Gogia S, Begiashvili V. Neoantigen-based immunotherapy: advancing precision medicine in cancer and glioblastoma treatment through discovery and innovation. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2025;6:1002313. [PMID: 40309350 PMCID: PMC12040680 DOI: 10.37349/etat.2025.1002313] [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: 01/29/2025] [Accepted: 04/07/2025] [Indexed: 05/02/2025]  Open
5
Zhang G, Zhou R. Integrating AI for next-generation cancer vaccine design. Sci Bull (Beijing) 2025:S2095-9273(25)00402-5. [PMID: 40368660 DOI: 10.1016/j.scib.2025.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2025]
6
George MM, Brennick CA, Hagymasi AT, Shcheglova TV, Al Seesi S, Rosales TJ, Baker BM, Mandoiu II, Srivastava PK. A frameshift-generated cancer neoepitope that controls tumor burden in prophylaxis as well as therapy. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2025:vkaf016. [PMID: 40209093 DOI: 10.1093/jimmun/vkaf016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Accepted: 01/10/2025] [Indexed: 04/12/2025]
7
Agoni C, Fernández-Díaz R, Timmons PB, Adelfio A, Gómez H, Shields DC. Molecular Modelling in Bioactive Peptide Discovery and Characterisation. Biomolecules 2025;15:524. [PMID: 40305228 PMCID: PMC12025251 DOI: 10.3390/biom15040524] [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: 12/21/2024] [Revised: 03/12/2025] [Accepted: 04/01/2025] [Indexed: 05/02/2025]  Open
8
Rademaker DT, Parizi FM, van Vreeswijk M, Eerden S, Marzella DF, Xue LC. Predicting reverse-bound peptide conformations in MHC Class II with PANDORA. Front Immunol 2025;16:1525576. [PMID: 40196118 PMCID: PMC11973093 DOI: 10.3389/fimmu.2025.1525576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2024] [Accepted: 02/24/2025] [Indexed: 04/09/2025]  Open
9
Le MHN, Nguyen PK, Nguyen TPT, Nguyen HQ, Tam DNH, Huynh HH, Huynh PK, Le NQK. An in-depth review of AI-powered advancements in cancer drug discovery. Biochim Biophys Acta Mol Basis Dis 2025;1871:167680. [PMID: 39837431 DOI: 10.1016/j.bbadis.2025.167680] [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: 10/18/2024] [Revised: 01/12/2025] [Accepted: 01/16/2025] [Indexed: 01/23/2025]
10
Garfinkle EAR, Mardis ER. Cancer Immunogenomics Approaches and Applications to Cancer Vaccines. Cancer J 2025;31:e0762. [PMID: 40126884 DOI: 10.1097/ppo.0000000000000762] [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: 06/12/2024] [Accepted: 01/17/2025] [Indexed: 03/26/2025]
11
Szczepski K, Jaremko Ł. AlphaFold and what is next: bridging functional, systems and structural biology. Expert Rev Proteomics 2025;22:45-58. [PMID: 39824781 DOI: 10.1080/14789450.2025.2456046] [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: 11/22/2024] [Revised: 01/13/2025] [Accepted: 01/16/2025] [Indexed: 01/20/2025]
12
Li K, Lauschke VM, Zhou Y. Molecular docking to investigate HLA-associated idiosyncratic drug reactions. Drug Metab Rev 2025;57:67-90. [PMID: 39811883 DOI: 10.1080/03602532.2025.2453521] [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: 12/03/2024] [Accepted: 01/09/2025] [Indexed: 01/16/2025]
13
Keen MM, Keith AD, Ortlund EA. Epitope mapping via in vitro deep mutational scanning methods and its applications. J Biol Chem 2025;301:108072. [PMID: 39674321 PMCID: PMC11783119 DOI: 10.1016/j.jbc.2024.108072] [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: 09/30/2024] [Revised: 12/04/2024] [Accepted: 12/09/2024] [Indexed: 12/16/2024]  Open
14
Ma X, Zhang J, Jiang Q, Li YX, Yang G. Human microbiome-derived peptide affects the development of experimental autoimmune encephalomyelitis via molecular mimicry. EBioMedicine 2025;111:105516. [PMID: 39724786 PMCID: PMC11732510 DOI: 10.1016/j.ebiom.2024.105516] [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: 07/31/2024] [Revised: 12/08/2024] [Accepted: 12/08/2024] [Indexed: 12/28/2024]  Open
15
Fasoulis R, Paliouras G, Kavraki LE. RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models. J Chem Inf Model 2024;64:8729-8742. [PMID: 39555889 PMCID: PMC11633655 DOI: 10.1021/acs.jcim.4c01278] [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: 07/19/2024] [Revised: 10/16/2024] [Accepted: 11/07/2024] [Indexed: 11/19/2024]
16
Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Patsahan T, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction. Biophys J 2024;123:2902-2909. [PMID: 38751115 PMCID: PMC11393670 DOI: 10.1016/j.bpj.2024.05.011] [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: 01/12/2024] [Revised: 04/13/2024] [Accepted: 05/10/2024] [Indexed: 05/28/2024]  Open
17
Agarwal V, McShan AC. The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins. Nat Chem Biol 2024;20:950-959. [PMID: 38907110 PMCID: PMC11956457 DOI: 10.1038/s41589-024-01638-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 04/29/2024] [Indexed: 06/23/2024]
18
Mondal A, Singh B, Felkner RH, Falco AD, Swapna GVT, Montelione GT, Roth MJ, Perez A. A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries. Angew Chem Int Ed Engl 2024;63:e202405767. [PMID: 38588243 PMCID: PMC11544546 DOI: 10.1002/anie.202405767] [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: 03/26/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
19
Gupta S, Sgourakis NG. A structure-guided approach to predict MHC-I restriction of T cell receptors for public antigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597418. [PMID: 38895339 PMCID: PMC11185663 DOI: 10.1101/2024.06.04.597418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
20
Koncz B, Balogh GM, Manczinger M. A journey to your self: The vague definition of immune self and its practical implications. Proc Natl Acad Sci U S A 2024;121:e2309674121. [PMID: 38722806 PMCID: PMC11161755 DOI: 10.1073/pnas.2309674121] [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: 06/10/2024]  Open
21
McMaster B, Thorpe C, Ogg G, Deane CM, Koohy H. Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity? Nat Methods 2024;21:766-776. [PMID: 38654083 DOI: 10.1038/s41592-024-02240-7] [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: 08/23/2023] [Accepted: 03/08/2024] [Indexed: 04/25/2024]
22
Ahn YM, Maddumage JC, Grant EJ, Chatzileontiadou DS, Perera WG, Baker BM, Szeto C, Gras S. The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific. Curr Res Struct Biol 2024;7:100148. [PMID: 38742159 PMCID: PMC11089313 DOI: 10.1016/j.crstbi.2024.100148] [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: 12/21/2023] [Revised: 04/11/2024] [Accepted: 04/28/2024] [Indexed: 05/16/2024]  Open
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