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For: Khan A, Cowen-Rivers AI, Grosnit A, Deik DGX, Robert PA, Greiff V, Smorodina E, Rawat P, Akbar R, Dreczkowski K, Tutunov R, Bou-Ammar D, Wang J, Storkey A, Bou-Ammar H. Toward real-world automated antibody design with combinatorial Bayesian optimization. Cell Rep Methods 2023;3:100374. [PMID: 36814835 PMCID: PMC9939385 DOI: 10.1016/j.crmeth.2022.100374] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/08/2022] [Accepted: 12/07/2022] [Indexed: 06/14/2023]
Number Cited by Other Article(s)
1
Benard-Valle M, Wouters Y, Ljungars A, Nguyen GTT, Ahmadi S, Ebersole TW, Dahl CH, Guadarrama-Martínez A, Jeppesen F, Eriksen H, Rodríguez-Barrera G, Boddum K, Jenkins TP, Bjørn SP, Schoffelen S, Voldborg BG, Alagón A, Laustsen AH. In vivo neutralization of coral snake venoms with an oligoclonal nanobody mixture in a murine challenge model. Nat Commun 2024;15:4310. [PMID: 38773068 PMCID: PMC11109316 DOI: 10.1038/s41467-024-48539-z] [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: 10/24/2023] [Accepted: 05/02/2024] [Indexed: 05/23/2024]  Open
2
Barton J, Gaspariunas A, Galson JD, Leem J. Building Representation Learning Models for Antibody Comprehension. Cold Spring Harb Perspect Biol 2024;16:a041462. [PMID: 38012013 PMCID: PMC10910360 DOI: 10.1101/cshperspect.a041462] [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: 11/29/2023]
3
Sedgwick R, Goertz JP, Stevens MM, Misener R, van der Wilk M. Transfer Learning Bayesian Optimization to Design Competitor DNA Molecules for Use in Diagnostic Assays. ARXIV 2024:arXiv:2402.17704v1. [PMID: 38463498 PMCID: PMC10925383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
4
Gallo E. Revolutionizing Synthetic Antibody Design: Harnessing Artificial Intelligence and Deep Sequencing Big Data for Unprecedented Advances. Mol Biotechnol 2024:10.1007/s12033-024-01064-2. [PMID: 38308755 DOI: 10.1007/s12033-024-01064-2] [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: 11/03/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
5
Colliandre L, Muller C. Bayesian Optimization in Drug Discovery. Methods Mol Biol 2024;2716:101-136. [PMID: 37702937 DOI: 10.1007/978-1-0716-3449-3_5] [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: 09/14/2023]
6
Mullin M, McClory J, Haynes W, Grace J, Robertson N, van Heeke G. Applications and challenges in designing VHH-based bispecific antibodies: leveraging machine learning solutions. MAbs 2024;16:2341443. [PMID: 38666503 PMCID: PMC11057648 DOI: 10.1080/19420862.2024.2341443] [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: 09/22/2023] [Accepted: 04/05/2024] [Indexed: 05/01/2024]  Open
7
Hu H. Quantum Computer Simulation of Protein Protonation. J Chem Theory Comput 2023;19:5671-5676. [PMID: 37555728 DOI: 10.1021/acs.jctc.3c00606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
8
Bauer J, Rajagopal N, Gupta P, Gupta P, Nixon AE, Kumar S. How can we discover developable antibody-based biotherapeutics? Front Mol Biosci 2023;10:1221626. [PMID: 37609373 PMCID: PMC10441133 DOI: 10.3389/fmolb.2023.1221626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 08/24/2023]  Open
9
Li L, Gupta E, Spaeth J, Shing L, Jaimes R, Engelhart E, Lopez R, Caceres RS, Bepler T, Walsh ME. Machine learning optimization of candidate antibody yields highly diverse sub-nanomolar affinity antibody libraries. Nat Commun 2023;14:3454. [PMID: 37308471 DOI: 10.1038/s41467-023-39022-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/23/2023] [Indexed: 06/14/2023]  Open
10
Parkinson J, Hard R, Wang W. The RESP AI model accelerates the identification of tight-binding antibodies. Nat Commun 2023;14:454. [PMID: 36709319 PMCID: PMC9884274 DOI: 10.1038/s41467-023-36028-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 01/13/2023] [Indexed: 01/30/2023]  Open
11
Fernández-Quintero ML, Ljungars A, Waibl F, Greiff V, Andersen JT, Gjølberg TT, Jenkins TP, Voldborg BG, Grav LM, Kumar S, Georges G, Kettenberger H, Liedl KR, Tessier PM, McCafferty J, Laustsen AH. Assessing developability early in the discovery process for novel biologics. MAbs 2023;15:2171248. [PMID: 36823021 PMCID: PMC9980699 DOI: 10.1080/19420862.2023.2171248] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/18/2023] [Indexed: 02/25/2023]  Open
12
Kakuzaki T, Koga H, Takizawa S, Metsugi S, Shiraiwa H, Sampei Z, Yoshida K, Tsunoda H, Teramoto R. Monte Carlo Thompson sampling-guided design for antibody engineering. MAbs 2023;15:2244214. [PMID: 37605371 PMCID: PMC10446805 DOI: 10.1080/19420862.2023.2244214] [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: 12/22/2022] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/23/2023]  Open
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