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For: Adams RM, Mora T, Walczak AM, Kinney JB. Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. eLife 2016;5. [PMID: 28035901 PMCID: PMC5268739 DOI: 10.7554/elife.23156] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/27/2016] [Indexed: 11/30/2022]  Open
Number Cited by Other Article(s)
1
Posfai A, Zhou J, McCandlish DM, Kinney JB. Gauge fixing for sequence-function relationships. PLoS Comput Biol 2025;21:e1012818. [PMID: 40111986 PMCID: PMC11957564 DOI: 10.1371/journal.pcbi.1012818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 01/22/2025] [Indexed: 03/22/2025]  Open
2
Monge M, Giovanetti SM, Ravishankar A, Sadhu MJ. Highly replicated experiments studying complex genotypes using nested DNA barcodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.18.643964. [PMID: 40166312 PMCID: PMC11956976 DOI: 10.1101/2025.03.18.643964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
3
Fryer T, Wolff DS, Overath MD, Schäfer E, Laustsen AH, Jenkins TP, Andersen C. Post-assembly Plasmid Amplification for Increased Transformation Yields in E. coli and S. cerevisiae. CHEM & BIO ENGINEERING 2025;2:87-96. [PMID: 40041006 PMCID: PMC11873849 DOI: 10.1021/cbe.4c00115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 10/30/2024] [Accepted: 11/03/2024] [Indexed: 03/06/2025]
4
Kirby MB, Petersen BM, Faris JG, Kells SP, Sprenger KG, Whitehead TA. Retrospective SARS-CoV-2 human antibody development trajectories are largely sparse and permissive. Proc Natl Acad Sci U S A 2025;122:e2412787122. [PMID: 39841142 PMCID: PMC11789010 DOI: 10.1073/pnas.2412787122] [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: 06/25/2024] [Accepted: 11/27/2024] [Indexed: 01/23/2025]  Open
5
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
6
Alpay BA, Desai MM. Effects of selection stringency on the outcomes of directed evolution. PLoS One 2024;19:e0311438. [PMID: 39401192 PMCID: PMC11472920 DOI: 10.1371/journal.pone.0311438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Accepted: 09/18/2024] [Indexed: 10/17/2024]  Open
7
Yu C, Lin X, Cheng Y, Xu J, Wang H, Yan Y, Huang Y, Liu L, Zhao W, Zhao Q, Wang J, Zhang L. AbDPP: Target-oriented antibody design with pretraining and prior biological structure knowledge. Proteins 2024;92:1147-1160. [PMID: 38441337 DOI: 10.1002/prot.26676] [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: 09/25/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 10/26/2024]
8
Taylor AL, Starr TN. Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant. Virus Evol 2024;10:veae067. [PMID: 39310091 PMCID: PMC11414647 DOI: 10.1093/ve/veae067] [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: 07/24/2024] [Revised: 08/20/2024] [Accepted: 08/28/2024] [Indexed: 09/25/2024]  Open
9
Son A, Park J, Kim W, Lee W, Yoon Y, Ji J, Kim H. Integrating Computational Design and Experimental Approaches for Next-Generation Biologics. Biomolecules 2024;14:1073. [PMID: 39334841 PMCID: PMC11430650 DOI: 10.3390/biom14091073] [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: 07/23/2024] [Revised: 08/13/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024]  Open
10
Taylor AL, Starr TN. Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604853. [PMID: 39091888 PMCID: PMC11291116 DOI: 10.1101/2024.07.23.604853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
11
Posfai A, Zhou J, McCandlish DM, Kinney JB. Gauge fixing for sequence-function relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593772. [PMID: 38798671 PMCID: PMC11118547 DOI: 10.1101/2024.05.12.593772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
12
Ornelas MY, Ouyang WO, Wu NC. A library-on-library screen reveals the breadth expansion landscape of a broadly neutralizing betacoronavirus antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597810. [PMID: 38915656 PMCID: PMC11195093 DOI: 10.1101/2024.06.06.597810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
13
Alpay BA, Desai MM. Effects of selection stringency on the outcomes of directed evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.09.598029. [PMID: 38895455 PMCID: PMC11185767 DOI: 10.1101/2024.06.09.598029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
14
Petersen BM, Kirby MB, Chrispens KM, Irvin OM, Strawn IK, Haas CM, Walker AM, Baumer ZT, Ulmer SA, Ayala E, Rhodes ER, Guthmiller JJ, Steiner PJ, Whitehead TA. An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries. Nat Commun 2024;15:3974. [PMID: 38730230 PMCID: PMC11087541 DOI: 10.1038/s41467-024-48072-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: 09/29/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024]  Open
15
Case M, Smith M, Vinh J, Thurber G. Machine learning to predict continuous protein properties from binary cell sorting data and map unseen sequence space. Proc Natl Acad Sci U S A 2024;121:e2311726121. [PMID: 38451939 PMCID: PMC10945751 DOI: 10.1073/pnas.2311726121] [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: 07/24/2023] [Accepted: 12/27/2023] [Indexed: 03/09/2024]  Open
16
Mock M, Langmead CJ, Grandsard P, Edavettal S, Russell A. Recent advances in generative biology for biotherapeutic discovery. Trends Pharmacol Sci 2024;45:255-267. [PMID: 38378385 DOI: 10.1016/j.tips.2024.01.003] [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: 11/30/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 02/22/2024]
17
Pun MN, Ivanov A, Bellamy Q, Montague Z, LaMont C, Bradley P, Otwinowski J, Nourmohammad A. Learning the shape of protein microenvironments with a holographic convolutional neural network. Proc Natl Acad Sci U S A 2024;121:e2300838121. [PMID: 38300863 PMCID: PMC10861886 DOI: 10.1073/pnas.2300838121] [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: 01/18/2023] [Accepted: 11/29/2023] [Indexed: 02/03/2024]  Open
18
Feng Y, Yi J, Yang L, Wang Y, Wen J, Zhao W, Kim P, Zhou X. COV2Var, a function annotation database of SARS-CoV-2 genetic variation. Nucleic Acids Res 2024;52:D701-D713. [PMID: 37897356 PMCID: PMC10767816 DOI: 10.1093/nar/gkad958] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023]  Open
19
Taylor AL, Starr TN. Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution. PLoS Pathog 2023;19:e1011901. [PMID: 38157379 PMCID: PMC10783747 DOI: 10.1371/journal.ppat.1011901] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/11/2024] [Accepted: 12/14/2023] [Indexed: 01/03/2024]  Open
20
Teo QW, Wang Y, Lv H, Tan TJC, Lei R, Mao KJ, Wu NC. Stringent and complex sequence constraints of an IGHV1-69 broadly neutralizing antibody to influenza HA stem. Cell Rep 2023;42:113410. [PMID: 37976161 PMCID: PMC10872586 DOI: 10.1016/j.celrep.2023.113410] [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: 07/27/2023] [Revised: 09/29/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]  Open
21
Banach BB, Pletnev S, Olia AS, Xu K, Zhang B, Rawi R, Bylund T, Doria-Rose NA, Nguyen TD, Fahad AS, Lee M, Lin BC, Liu T, Louder MK, Madan B, McKee K, O'Dell S, Sastry M, Schön A, Bui N, Shen CH, Wolfe JR, Chuang GY, Mascola JR, Kwong PD, DeKosky BJ. Antibody-directed evolution reveals a mechanism for enhanced neutralization at the HIV-1 fusion peptide site. Nat Commun 2023;14:7593. [PMID: 37989731 PMCID: PMC10663459 DOI: 10.1038/s41467-023-42098-5] [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: 12/23/2022] [Accepted: 09/25/2023] [Indexed: 11/23/2023]  Open
22
Taylor AL, Starr TN. Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557279. [PMID: 37745441 PMCID: PMC10515859 DOI: 10.1101/2023.09.11.557279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
23
Xie X, Sun X, Wang Y, Lehner B, Li X. Dominance vs epistasis: the biophysical origins and plasticity of genetic interactions within and between alleles. Nat Commun 2023;14:5551. [PMID: 37689712 PMCID: PMC10492795 DOI: 10.1038/s41467-023-41188-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/25/2023] [Indexed: 09/11/2023]  Open
24
Smith MD, Case MA, Makowski EK, Tessier PM. Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data. Bioinformatics 2023;39:btad446. [PMID: 37478351 PMCID: PMC10477941 DOI: 10.1093/bioinformatics/btad446] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/21/2023] [Accepted: 07/20/2023] [Indexed: 07/23/2023]  Open
25
Teo QW, Wang Y, Lv H, Tan TJ, Lei R, Mao KJ, Wu NC. Stringent and complex sequence constraints of an IGHV1-69 broadly neutralizing antibody to influenza HA stem. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.547908. [PMID: 37461670 PMCID: PMC10350038 DOI: 10.1101/2023.07.06.547908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
26
Pan X, López Acevedo SN, Cuziol C, De Tavernier E, Fahad AS, Longjam PS, Rao SP, Aguilera-Rodríguez D, Rezé M, Bricault CA, Gutiérrez-González MF, de Souza MO, DiNapoli JM, Vigne E, Shahsavarian MA, DeKosky BJ. Large-scale antibody immune response mapping of splenic B cells and bone marrow plasma cells in a transgenic mouse model. Front Immunol 2023;14:1137069. [PMID: 37346047 PMCID: PMC10280637 DOI: 10.3389/fimmu.2023.1137069] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/30/2023] [Indexed: 06/23/2023]  Open
27
Moulana A, Dupic T, Phillips AM, Desai MM. Genotype-phenotype landscapes for immune-pathogen coevolution. Trends Immunol 2023;44:384-396. [PMID: 37024340 PMCID: PMC10147585 DOI: 10.1016/j.it.2023.03.006] [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: 02/03/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 04/07/2023]
28
Chandra S, Manjunath K, Asok A, Varadarajan R. Mutational scan inferred binding energetics and structure in intrinsically disordered protein CcdA. Protein Sci 2023;32:e4580. [PMID: 36714997 PMCID: PMC9951195 DOI: 10.1002/pro.4580] [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: 08/29/2022] [Revised: 01/02/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
29
Moulana A, Dupic T, Phillips AM, Chang J, Roffler AA, Greaney AJ, Starr TN, Bloom JD, Desai MM. The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution. eLife 2023;12:e83442. [PMID: 36803543 PMCID: PMC9949795 DOI: 10.7554/elife.83442] [Citation(s) in RCA: 24] [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: 09/13/2022] [Accepted: 02/06/2023] [Indexed: 02/16/2023]  Open
30
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 REPORTS METHODS 2023;3:100374. [PMID: 36814835 PMCID: PMC9939385 DOI: 10.1016/j.crmeth.2022.100374] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/08/2022] [Accepted: 12/07/2022] [Indexed: 06/14/2023]
31
Phillips AM, Maurer DP, Brooks C, Dupic T, Schmidt AG, Desai MM. Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody. eLife 2023;12:83628. [PMID: 36625542 PMCID: PMC9995116 DOI: 10.7554/elife.83628] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/09/2023] [Indexed: 01/11/2023]  Open
32
Chattopadhyay G, Ahmed S, Srilatha NS, Asok A, Varadarajan R. Ter-Seq: A high-throughput method to stabilize transient ternary complexes and measure associated kinetics. Protein Sci 2023;32:e4514. [PMID: 36382921 PMCID: PMC9793979 DOI: 10.1002/pro.4514] [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: 09/09/2022] [Revised: 11/01/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
33
Zambo B, Morlet B, Negroni L, Trave G, Gogl G. Native holdup (nHU) to measure binding affinities from cell extracts. SCIENCE ADVANCES 2022;8:eade3828. [PMID: 36542723 PMCID: PMC9770967 DOI: 10.1126/sciadv.ade3828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
34
Moulana A, Dupic T, Phillips AM, Chang J, Nieves S, Roffler AA, Greaney AJ, Starr TN, Bloom JD, Desai MM. Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1. Nat Commun 2022;13:7011. [PMID: 36384919 PMCID: PMC9668218 DOI: 10.1038/s41467-022-34506-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022]  Open
35
Starr TN, Greaney AJ, Stewart CM, Walls AC, Hannon WW, Veesler D, Bloom JD. Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains. PLoS Pathog 2022;18:e1010951. [PMID: 36399443 PMCID: PMC9674177 DOI: 10.1371/journal.ppat.1010951] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022]  Open
36
Trippe BL, Huang B, DeBenedictis EA, Coventry B, Bhattacharya N, Yang KK, Baker D, Crawford L. Randomized gates eliminate bias in sort‐seq assays. Protein Sci 2022. [PMCID: PMC9601873 DOI: 10.1002/pro.4401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
37
Banach BB, Tripathi P, Da Silva Pereira L, Gorman J, Nguyen TD, Dillon M, Fahad AS, Kiyuka PK, Madan B, Wolfe JR, Bonilla B, Flynn B, Francica JR, Hurlburt NK, Kisalu NK, Liu T, Ou L, Rawi R, Schön A, Shen CH, Teng IT, Zhang B, Pancera M, Idris AH, Seder RA, Kwong PD, DeKosky BJ. Highly protective antimalarial antibodies via precision library generation and yeast display screening. J Exp Med 2022;219:e20220323. [PMID: 35736810 PMCID: PMC9242090 DOI: 10.1084/jem.20220323] [Citation(s) in RCA: 9] [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: 02/21/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/03/2023]  Open
38
Starr TN, Greaney AJ, Hannon WW, Loes AN, Hauser K, Dillen JR, Ferri E, Farrell AG, Dadonaite B, McCallum M, Matreyek KA, Corti D, Veesler D, Snell G, Bloom JD. Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution. Science 2022;377:420-424. [PMID: 35762884 PMCID: PMC9273037 DOI: 10.1126/science.abo7896] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/23/2022] [Indexed: 12/30/2022]
39
Makowski EK, Kinnunen PC, Huang J, Wu L, Smith MD, Wang T, Desai AA, Streu CN, Zhang Y, Zupancic JM, Schardt JS, Linderman JJ, Tessier PM. Co-optimization of therapeutic antibody affinity and specificity using machine learning models that generalize to novel mutational space. Nat Commun 2022;13:3788. [PMID: 35778381 PMCID: PMC9249733 DOI: 10.1038/s41467-022-31457-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/20/2022] [Indexed: 11/08/2022]  Open
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Chattopadhyay G, Bhasin M, Ahmed S, Gosain TP, Ganesan S, Das S, Thakur C, Chandra N, Singh R, Varadarajan R. Functional and Biochemical Characterization of the MazEF6 Toxin-Antitoxin System of Mycobacterium tuberculosis. J Bacteriol 2022;204:e0005822. [PMID: 35357163 PMCID: PMC9053165 DOI: 10.1128/jb.00058-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/07/2022] [Indexed: 12/15/2022]  Open
41
Faure AJ, Domingo J, Schmiedel JM, Hidalgo-Carcedo C, Diss G, Lehner B. Mapping the energetic and allosteric landscapes of protein binding domains. Nature 2022;604:175-183. [PMID: 35388192 DOI: 10.1038/s41586-022-04586-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
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Starr TN, Zepeda SK, Walls AC, Greaney AJ, Alkhovsky S, Veesler D, Bloom JD. ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Nature 2022;603:913-918. [PMID: 35114688 PMCID: PMC8967715 DOI: 10.1038/s41586-022-04464-z] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/25/2022] [Indexed: 11/08/2022]
43
Zhou Y, Yuan Y, Wu Y, Li L, Jameel A, Xing XH, Zhang C. Encoding Genetic Circuits with DNA Barcodes Paves the Way for Machine Learning-Assisted Metabolite Biosensor Response Curve Profiling in Yeast. ACS Synth Biol 2022;11:977-989. [PMID: 35089702 DOI: 10.1021/acssynbio.1c00595] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hwang T, Parker SS, Hill SM, Grant RA, Ilunga MW, Sivaraman V, Mouneimne G, Keating AE. Native proline-rich motifs exploit sequence context to target actin-remodeling Ena/VASP protein ENAH. eLife 2022;11:70680. [PMID: 35076015 PMCID: PMC8789275 DOI: 10.7554/elife.70680] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 01/06/2022] [Indexed: 12/13/2022]  Open
45
Javanmardi K, Chou CW, Terrace CI, Annapareddy A, Kaoud TS, Guo Q, Lutgens J, Zorkic H, Horton AP, Gardner EC, Nguyen G, Boutz DR, Goike J, Voss WN, Kuo HC, Dalby KN, Gollihar JD, Finkelstein IJ. Rapid characterization of spike variants via mammalian cell surface display. Mol Cell 2021;81:5099-5111.e8. [PMID: 34919820 PMCID: PMC8675084 DOI: 10.1016/j.molcel.2021.11.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022]
46
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: 27] [Impact Index Per Article: 6.8] [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]
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Francino-Urdaniz IM, Whitehead TA. An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies. RSC Chem Biol 2021;2:1580-1589. [PMID: 34977572 PMCID: PMC8637828 DOI: 10.1039/d1cb00169h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/25/2021] [Indexed: 12/20/2022]  Open
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Neutralizing Monoclonal Antibodies That Target the Spike Receptor Binding Domain Confer Fc Receptor-Independent Protection against SARS-CoV-2 Infection in Syrian Hamsters. mBio 2021;12:e0239521. [PMID: 34517754 PMCID: PMC8546861 DOI: 10.1128/mbio.02395-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
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Phillips AM, Lawrence KR, Moulana A, Dupic T, Chang J, Johnson MS, Cvijovic I, Mora T, Walczak AM, Desai MM. Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies. eLife 2021;10:71393. [PMID: 34491198 PMCID: PMC8476123 DOI: 10.7554/elife.71393] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/05/2021] [Indexed: 12/12/2022]  Open
50
Coyote-Maestas W, Fraser JS. ORACLE reveals a bright future to fight bacteria. eLife 2021;10:68277. [PMID: 33856343 PMCID: PMC8049741 DOI: 10.7554/elife.68277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 04/09/2021] [Indexed: 11/13/2022]  Open
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