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For: Graves J, Byerly J, Priego E, Makkapati N, Parish SV, Medellin B, Berrondo M. A Review of Deep Learning Methods for Antibodies. Antibodies (Basel) 2020;9:E12. [PMID: 32354020 PMCID: PMC7344881 DOI: 10.3390/antib9020012] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/09/2023]  Open
Number Cited by Other Article(s)
1
Kalejaye L, Wu IE, Terry T, Lai PK. DeepSP: Deep learning-based spatial properties to predict monoclonal antibody stability. Comput Struct Biotechnol J 2024;23:2220-2229. [PMID: 38827232 PMCID: PMC11140563 DOI: 10.1016/j.csbj.2024.05.029] [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: 03/02/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/04/2024]  Open
2
Joubbi S, Micheli A, Milazzo P, Maccari G, Ciano G, Cardamone D, Medini D. Antibody design using deep learning: from sequence and structure design to affinity maturation. Brief Bioinform 2024;25:bbae307. [PMID: 38960409 PMCID: PMC11221890 DOI: 10.1093/bib/bbae307] [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: 03/03/2024] [Revised: 05/20/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]  Open
3
Zhang X, Wang H, Sun C. BiSpec Pairwise AI: guiding the selection of bispecific antibody target combinations with pairwise learning and GPT augmentation. J Cancer Res Clin Oncol 2024;150:237. [PMID: 38713378 PMCID: PMC11076393 DOI: 10.1007/s00432-024-05740-3] [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: 02/18/2024] [Accepted: 04/03/2024] [Indexed: 05/08/2024]
4
Éliás S, Wrzodek C, Deane CM, Tissot AC, Klostermann S, Ros F. Prediction of polyspecificity from antibody sequence data by machine learning. FRONTIERS IN BIOINFORMATICS 2024;3:1286883. [PMID: 38651055 PMCID: PMC11033685 DOI: 10.3389/fbinf.2023.1286883] [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: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 04/25/2024]  Open
5
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
6
Grąźlewska W, Sołowińska K, Holec-Gąsior L. In silico epitope prediction of Borrelia burgdorferi sensu lato antigens for the detection of specific antibodies. J Immunol Methods 2024;524:113596. [PMID: 38070727 DOI: 10.1016/j.jim.2023.113596] [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: 11/16/2022] [Revised: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023]
7
Zeng X, Wang T, Kang Y, Bai G, Ma B. Evaluation of Molecular Simulations and Deep Learning Prediction of Antibodies' Recognition of TRBC1 and TRBC2. Antibodies (Basel) 2023;12:58. [PMID: 37753972 PMCID: PMC10525649 DOI: 10.3390/antib12030058] [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: 08/12/2023] [Revised: 08/25/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]  Open
8
Li J, Kang G, Wang J, Yuan H, Wu Y, Meng S, Wang P, Zhang M, Wang Y, Feng Y, Huang H, de Marco A. Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization. Int J Biol Macromol 2023;247:125733. [PMID: 37423452 DOI: 10.1016/j.ijbiomac.2023.125733] [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: 04/03/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
9
Guarra F, Colombo G. Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens. J Chem Theory Comput 2023;19:5315-5333. [PMID: 37527403 PMCID: PMC10448727 DOI: 10.1021/acs.jctc.3c00513] [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: 05/17/2023] [Indexed: 08/03/2023]
10
Moingeon P. Artificial intelligence-driven drug development against autoimmune diseases. Trends Pharmacol Sci 2023;44:411-424. [PMID: 37268540 DOI: 10.1016/j.tips.2023.04.005] [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: 03/19/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 06/04/2023]
11
Zhou Y, Huang Z, Gou Y, Liu S, Yang W, Zhang H, Dzisoo AM, Huang J. AB-Amy: machine learning aided amyloidogenic risk prediction of therapeutic antibody light chains. Antib Ther 2023;6:147-156. [PMID: 37492587 PMCID: PMC10365155 DOI: 10.1093/abt/tbad007] [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: 10/26/2022] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 07/27/2023]  Open
12
Helleckes LM, Hemmerich J, Wiechert W, von Lieres E, Grünberger A. Machine learning in bioprocess development: from promise to practice. Trends Biotechnol 2023;41:817-835. [PMID: 36456404 DOI: 10.1016/j.tibtech.2022.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022]
13
Li T, Li Y, Zhu X, He Y, Wu Y, Ying T, Xie Z. Artificial intelligence in cancer immunotherapy: Applications in neoantigen recognition, antibody design and immunotherapy response prediction. Semin Cancer Biol 2023;91:50-69. [PMID: 36870459 DOI: 10.1016/j.semcancer.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
14
Lee FS, Anderson AG, Olafson BD. Benchmarking TriadAb using targets from the second antibody modeling assessment. Protein Eng Des Sel 2023;36:gzad013. [PMID: 37864287 DOI: 10.1093/protein/gzad013] [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: 05/05/2023] [Revised: 08/10/2023] [Indexed: 10/22/2023]  Open
15
Dănăilă VR, Avram S, Buiu C. The applications of machine learning in HIV neutralizing antibodies research-A systematic review. Artif Intell Med 2022;134:102429. [PMID: 36462896 DOI: 10.1016/j.artmed.2022.102429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 09/03/2022] [Accepted: 10/13/2022] [Indexed: 12/14/2022]
16
Gopal R, Fitzpatrick E, Pentakota N, Jayaraman A, Tharakaraman K, Capila I. Optimizing Antibody Affinity and Developability Using a Framework-CDR Shuffling Approach-Application to an Anti-SARS-CoV-2 Antibody. Viruses 2022;14:v14122694. [PMID: 36560698 PMCID: PMC9784564 DOI: 10.3390/v14122694] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]  Open
17
Wilman W, Wróbel S, Bielska W, Deszynski P, Dudzic P, Jaszczyszyn I, Kaniewski J, Młokosiewicz J, Rouyan A, Satława T, Kumar S, Greiff V, Krawczyk K. Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery. Brief Bioinform 2022;23:6643456. [PMID: 35830864 PMCID: PMC9294429 DOI: 10.1093/bib/bbac267] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022]  Open
18
Antibody structure prediction using interpretable deep learning. PATTERNS (NEW YORK, N.Y.) 2022;3:100406. [PMID: 35199061 PMCID: PMC8848015 DOI: 10.1016/j.patter.2021.100406] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022]
19
Khetan R, Curtis R, Deane CM, Hadsund JT, Kar U, Krawczyk K, Kuroda D, Robinson SA, Sormanni P, Tsumoto K, Warwicker J, Martin ACR. Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics. MAbs 2022;14:2020082. [PMID: 35104168 PMCID: PMC8812776 DOI: 10.1080/19420862.2021.2020082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
20
Akbar R, Robert PA, Weber CR, Widrich M, Frank R, Pavlović M, Scheffer L, Chernigovskaya M, Snapkov I, Slabodkin A, Mehta BB, Miho E, Lund-Johansen F, Andersen JT, Hochreiter S, Hobæk Haff I, Klambauer G, Sandve GK, Greiff V. In silico proof of principle of machine learning-based antibody design at unconstrained scale. MAbs 2022;14:2031482. [PMID: 35377271 PMCID: PMC8986205 DOI: 10.1080/19420862.2022.2031482] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
21
Hanning KR, Minot M, Warrender AK, Kelton W, Reddy ST. Deep mutational scanning for therapeutic antibody engineering. Trends Pharmacol Sci 2021;43:123-135. [PMID: 34895944 DOI: 10.1016/j.tips.2021.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022]
22
Lin X, Wang G, Ma L, Liu G. Study on Factors Affecting the Performance of a CRISPR/Cas-Assisted New Immunoassay: Detection of Salivary Insulin as an Example. Front Bioeng Biotechnol 2021;9:752514. [PMID: 34858958 PMCID: PMC8632245 DOI: 10.3389/fbioe.2021.752514] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022]  Open
23
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00413-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
24
Pedrioli A, Oxenius A. Single B cell technologies for monoclonal antibody discovery. Trends Immunol 2021;42:1143-1158. [PMID: 34743921 DOI: 10.1016/j.it.2021.10.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022]
25
Mak KK, Balijepalli MK, Pichika MR. Success stories of AI in drug discovery - where do things stand? Expert Opin Drug Discov 2021;17:79-92. [PMID: 34553659 DOI: 10.1080/17460441.2022.1985108] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
26
Schneider C, Buchanan A, Taddese B, Deane CM. DLAB: deep learning methods for structure-based virtual screening of antibodies. Bioinformatics 2021;38:377-383. [PMID: 34546288 PMCID: PMC8723137 DOI: 10.1093/bioinformatics/btab660] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/03/2021] [Accepted: 09/01/2021] [Indexed: 02/03/2023]  Open
27
Prabakaran P, Rao SP, Wendt M. Animal immunization merges with innovative technologies: A new paradigm shift in antibody discovery. MAbs 2021;13:1924347. [PMID: 33947305 PMCID: PMC8118498 DOI: 10.1080/19420862.2021.1924347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
28
Pertseva M, Gao B, Neumeier D, Yermanos A, Reddy ST. Applications of Machine and Deep Learning in Adaptive Immunity. Annu Rev Chem Biomol Eng 2021;12:39-62. [PMID: 33852352 DOI: 10.1146/annurev-chembioeng-101420-125021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
29
Gao W, Mahajan SP, Sulam J, Gray JJ. Deep Learning in Protein Structural Modeling and Design. PATTERNS (NEW YORK, N.Y.) 2020;1:100142. [PMID: 33336200 PMCID: PMC7733882 DOI: 10.1016/j.patter.2020.100142] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
30
Greiff V, Yaari G, Cowell LG. Mining adaptive immune receptor repertoires for biological and clinical information using machine learning. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.coisb.2020.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
31
Pomés A, Mueller GA, Chruszcz M. Structural Aspects of the Allergen-Antibody Interaction. Front Immunol 2020;11:2067. [PMID: 32983155 PMCID: PMC7492603 DOI: 10.3389/fimmu.2020.02067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/29/2020] [Indexed: 12/23/2022]  Open
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