De novo protein design enables the precise induction of RSV-neutralizing antibodies
Open accessAbstract
TopoBuilding precision vaccines: To induce strong and targeted neutralizing antibody (nAb) responses against vaccine targets, one strategy has been to use computationally designed immunogens. However, the structural complexity of many known neutralization epitopes has posed a major challenge for the design of accurate epitope mimetics. Sesterhenn et al. created a protein design algorithm called TopoBuilder to design scaffolds for irregular and discontinuous neutralization epitopes. As a proof of principle, the authors generated epitope-focused immunogens based on the prefusion conformation of the respiratory syncytial virus (RSV) fusion protein. When these immunogens were used to vaccinate mice and nonhuman primates in RSV infection models, they generated targeted nAb responses to RSV and boosted site-specific nAb responses in heterologous prime-boost vaccination schemes. Science , this issue p. eaay5051
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An in silico benchmark test comprising 25 motif-scaffolding design problems addressed in six recent publications was established to evaluate motif-scaffolding methods.
“we established an in silico benchmark test (Supplementary Table 9) comprising 25 motif-scaffolding design problems addressed in six recent publications encompassing several design methodologies4,5,29,38–40”
From De novo design of protein structure and function with RFdiffusion (2023) · cites this paper as [38]
With the exception of helical bundles, previous methods do not extend readily to more complex functional sites composed of three or more chain segments.
“Previous methods can scaffold functional sites made up of one or two contiguous chain segments (6–10), but with the exception of helical bundles (8) these do not extend readily to more complex sites composed of three or more chain segments, and the generated backbones are not guaranteed to be designable (encodable by some amino acid sequence).”
From Scaffolding protein functional sites using deep learning (2022) · cites this paper as [9]
Previous methods can scaffold functional sites made up of one or two contiguous chain segments.
“Previous methods can scaffold functional sites made up of one or two contiguous chain segments (6–10), but with the exception of helical bundles (8) these do not extend readily to more complex sites composed of three or more chain segments, and the generated backbones are not guaranteed to be designable (encodable by some amino acid sequence).”
From Scaffolding protein functional sites using deep learning (2022) · cites this paper as [9]
The backbones generated by previous functional-site scaffolding methods are not guaranteed to be designable.
“Previous methods can scaffold functional sites made up of one or two contiguous chain segments (6–10), but with the exception of helical bundles (8) these do not extend readily to more complex sites composed of three or more chain segments, and the generated backbones are not guaranteed to be designable (encodable by some amino acid sequence).”
From Scaffolding protein functional sites using deep learning (2022) · cites this paper as [9]
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Features and development of Coot
Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. D. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 27,510 · see citing works
<i>PHENIX</i> : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716 · see citing works
<i>Phaser</i> crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612 · see citing works
Kabsch, W. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909047337 · Cited by 16,463 · see citing works
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Punjani, A., Rubinstein, J. L., Fleet, D. J., & Brubaker, M. A. (2017) · Nature Methods · doi:10.1038/nmeth.4169 · Cited by 9,168 · see citing works
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkòczi, G., Chen, V. B., Davis, I., Echols, N., Headd, J. J., Hung, L., Kapral, G. J., Grosse‐Kunstleve, R. W., et al. (2012) · International Tables for Crystallography · doi:10.1107/97809553602060000865 · Cited by 7,334 · see citing works
RELION: Implementation of a Bayesian approach to cryo-EM structure determination
Scheres, S. H. W. (2012) · Journal of Structural Biology · doi:10.1016/j.jsb.2012.09.006 · Cited by 5,446 · see citing works
CTFFIND4: Fast and accurate defocus estimation from electron micrographs
Rohou, A. L., & Grigorieff, N. (2015) · Journal of Structural Biology · doi:10.1016/j.jsb.2015.08.008 · Cited by 4,926 · see citing works
Principles of protein-protein interactions
Jones, S., & Thornton, J. M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.1.13 · Cited by 2,684 · see citing works
Linking Crystallographic Model and Data Quality
Karplus, P. A., & Diederichs, K. (2012) · Science · doi:10.1126/science.1218231 · Cited by 1,781 · see citing works
Sattler, M. (1999) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/s0079-6565(98)00025-9 · Cited by 1,770 · see citing works
The coming of age of de novo protein design
Huang, P.-S., Boyken, S. E., & Baker, D. (2016) · Nature · doi:10.1038/nature19946 · Cited by 1,478 · see citing works
Herrmann, T., Güntert, P., & Wüthrich, K. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00241-3 · Cited by 1,464 · see citing works
Corti, D., Voss, J., Gamblin, S. J., Codoni, G., Macagno, A., Jarrossay, D., Vachieri, S. G., Pinna, D., Minola, A., Vanzetta, F., et al. (2011) · Science · doi:10.1126/science.1205669 · Cited by 1,203 · see citing works
Structure-Based Design of a Fusion Glycoprotein Vaccine for Respiratory Syncytial Virus
McLellan, J. S., Chen, M., Joyce, M. G., Sastry, M., Stewart-Jones, G. B. E., Yang, Y., Zhang, B., Chen, L., Srivatsan, S., Zheng, A., et al. (2013) · Science · doi:10.1126/science.1243283 · Cited by 1,126 · see citing works
Shen, Y., & Bax, A. (2013) · Journal of Biomolecular NMR · doi:10.1007/s10858-013-9741-y · Cited by 1,123 · see citing works
Tiller, T., Meffre, E., Yurasov, S., Tsuiji, M., Nussenzweig, M. C., & Wardemann, H. (2007) · Journal of Immunological Methods · doi:10.1016/j.jim.2007.09.017 · Cited by 1,078 · see citing works
Isolating and engineering human antibodies using yeast surface display
Chao, G., Lau, W. L., Hackel, B. J., Sazinsky, S. L., Lippow, S. M., & Wittrup, K. D. (2006) · Nature Protocols · doi:10.1038/nprot.2006.94 · Cited by 913 · see citing works
Dejnirattisai, W., Supasa, P., Wongwiwat, W., Rouvinski, A., Spaeth, G. B., Duangchinda, T., Sakuntabhai, A., Cao‐Lormeau, V., Malasit, P., Rey, F. A., et al. (2016) · Nature Immunology · doi:10.1038/ni.3515 · Cited by 907 · see citing works
Structure of RSV Fusion Glycoprotein Trimer Bound to a Prefusion-Specific Neutralizing Antibody
McLellan, J. S., Chen, M., Leung, S., Graepel, K. W., Du, X., Yang, Y., Zhou, T., Baxa, U., Yasuda, E., Beaumont, T., et al. (2013) · Science · doi:10.1126/science.1234914 · Cited by 883 · see citing works
Johnson, S., Oliver, C. N., Prince, G. A., Hemming, V. G., Pfarr, D. S., Wang, S., Dormitzer, M., O'Grady, J., Koenig, S., Tamura, J. K., et al. (1997) · The Journal of Infectious Diseases · doi:10.1086/514115 · Cited by 642 · see citing works
de la Rosa-Trevin, J. M., Quintana, A., del Caño, L., Zaldívar-Peraza, A., Foche, I., Gutiérrez, J., Gómez-Blanco, J., Burguet–Castell, J., Cuenca-Alba, J., Abrishami, V., et al. (2016) · Journal of Structural Biology · doi:10.1016/j.jsb.2016.04.010 · Cited by 594 · see citing works
Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
Fleishman, S. J., Whitehead, T. A., Ekiert, D. C., Dreyfus, C., Corn, J. E., Strauch, E.-M., Wilson, I. A., & Baker, D. (2011) · Science · doi:10.1126/science.1202617 · Cited by 585 · see citing works
Principles for designing ideal protein structures
Koga, N., Tatsumi-Koga, R., Liu, G., Xiao, R., Acton, T. B., Montelione, G. T., & Baker, D. (2012) · Nature · doi:10.1038/nature11600 · Cited by 564 · see citing works
Proof of principle for epitope-focused vaccine design
Correia, B. E., Bates, J. T., Loomis, R. J., Baneyx, G., Carrico, C., Jardine, J. G., Rupert, P., Correnti, C., Kalyuzhniy, O., Vittal, V., et al. (2014) · Nature · doi:10.1038/nature12966 · Cited by 555 · see citing works
Self-citationStructural basis of potent Zika–dengue virus antibody cross-neutralization
Spaeth, G. B., Dejnirattisai, W., Rouvinski, A., Vaney, M. C., Medits, I., Sharma, A., Simon‐Lorière, E., Sakuntabhai, A., Cao‐Lormeau, V., Haouz, A., et al. (2016) · Nature · doi:10.1038/nature18938 · Cited by 534 · see citing works
De novo design of potent and selective mimics of IL-2 and IL-15
Silva, D.-A., Yu, S., Ulge, U. Y., Spangler, J. B., Jude, K. M., Labão-Almeida, C., Ali, L. R., Quijano-Rubio, A., Ruterbusch, M., Leung, I., et al. (2019) · Nature · doi:10.1038/s41586-018-0830-7 · Cited by 531 · see citing works
Herrmann, T., Güntert, P., & Wüthrich, K. (2002) · Journal of Biomolecular NMR · doi:10.1023/a:1021614115432 · Cited by 482 · see citing works
Massively parallel de novo protein design for targeted therapeutics
Chevalier, A., Silva, D.-A., Rocklin, G. J., Hicks, D. R., Vergara, R., Murapa, P., Bernard, S. M., Zhang, L., Lam, K.-H., Yao, G., et al. (2017) · Nature · doi:10.1038/nature23912 · Cited by 453 · cited 3× · see citing works
“3B), an effective method to digest partially unfolded proteins (7, 38).”
BackgroundMethodHIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen
Jardine, J. G., Kulp, D. W., Havenar‐Daughton, C., Sarkar, A., Briney, B. S., Sok, D., Sesterhenn, F., Ereño‐Orbea, J., Kalyuzhniy, O., Deresa, I., et al. (2016) · Science · doi:10.1126/science.aad9195 · Cited by 451 · see citing works
Self-citationMarcandalli, J., Fiala, B., Ols, S., Perotti, M., de van der Schueren, W., Snijder, J., Hodge, E. A., Benhaim, M. A., Ravichandran, R., Carter, L. P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.046 · Cited by 439 · see citing works
Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design
Rappuoli, R., Bottomley, M. J., D’Oro, U., Finco, O., & Gregorio, E. D. (2016) · The Journal of Experimental Medicine · doi:10.1084/jem.20151960 · Cited by 438 · see citing works
Prefusion F–specific antibodies determine the magnitude of RSV neutralizing activity in human sera
Ngwuta, J. O., Chen, M., Modjarrad, K., Joyce, M. G., Kanekiyo, M., Kumar, A., Yassine, H. M., Moin, S. M., Killikelly, A. M., Chuang, G., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aac4241 · Cited by 433 · see citing works
Immune history profoundly affects broadly protective B cell responses to influenza
Andrews, S. F., Huang, Y., Kaur, K., Popova, L. I., Ho, I. Y., Pauli, N. T., Henry, C., Taylor, W. M., Lim, S., Huang, M., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aad0522 · Cited by 413 · see citing works
Relaxation of backbone bond geometry improves protein energy landscape modeling
Conway, P., Tyka, M. D., DiMaio, F., Konerding, D. E., & Baker, D. A. (2013) · Protein Science · doi:10.1002/pro.2389 · Cited by 408 · see citing works
Recent progress in broadly neutralizing antibodies to HIV
Sok, D., & Burton, D. R. (2018) · Nature Immunology · doi:10.1038/s41590-018-0235-7 · Cited by 406 · see citing works
A proof of concept for structure-based vaccine design targeting RSV in humans
Crank, M. C., Ruckwardt, T. J., Chen, M., Morabito, K. M., Phung, E., Costner, P. J., Holman, L. A., Hickman, S. P., Berkowitz, N. M., Gordon, I. J., et al. (2019) · Science · doi:10.1126/science.aav9033 · Cited by 333 · see citing works
Xu, K. Y., Acharya, P., Kong, R., Cheng, C., Chuang, G., Liu, K., Louder, M. K., O'Dell, S. J., Rawi, R., Sastry, M., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0042-6 · Cited by 284 · see citing works
Self-citationElicitation of structure-specific antibodies by epitope scaffolds
Ofek, G., Guenaga, F. J., Schief, W. R., Skinner, J., Baker, D., Wyatt, R., & Kwong, P. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1004728107 · Cited by 278 · see citing works
Cross-neutralization of four paramyxoviruses by a human monoclonal antibody
Corti, D., Bianchi, S., Zatta, F., Minola, A., Perez, L. H., Agatic, G., Guarino, B., Silacci, C., Marcandalli, J., Marsland, B. J., et al. (2013) · Nature · doi:10.1038/nature12442 · Cited by 274 · see citing works
Structural and genetic basis for development of broadly neutralizing influenza antibodies
Lingwood, D., McTamney, P. M., Yassine, H. M., Whittle, J. R. R., Guo, X., Boyington, J. C., Wei, C., & Nabel, G. J. (2012) · Nature · doi:10.1038/nature11371 · Cited by 269 · see citing works
Defining B cell immunodominance to viruses
Angeletti, D., Gibbs, J. S., Angel, M., Košík, I., Hickman, H. D., Frank, G. M., Das, S. R., Wheatley, A. K., Prabhakaran, M. S., Leggat, D. J., et al. (2017) · Nature Immunology · doi:10.1038/ni.3680 · Cited by 257 · see citing works
Tailored Immunogens Direct Affinity Maturation toward HIV Neutralizing Antibodies
Briney, B. S., Sok, D., Jardine, J. G., Kulp, D. W., Skog, P. D., Menis, S., Jacak, R., Kalyuzhniy, O., de Val, N., Sesterhenn, F., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.005 · Cited by 255 · see citing works
Self-citationDe novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy
Huang, P., Feldmeier, K., Parmeggiani, F., Fernández‐Velasco, D. A., Höcker, B., & Baker, D. A. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1966 · Cited by 253 · see citing works
Exploring the repeat protein universe through computational protein design
Brunette, T., Parmeggiani, F., Huang, P., Bhabha, G., Ekiert, D. C., Tsutakawa, S. E., Hura, G. L., Tainer, J. A., & Baker, D. A. (2015) · Nature · doi:10.1038/nature16162 · Cited by 252 · see citing works
Computational characterization of B-cell epitopes
Rubinstein, N. D., Mayrose, I., Halperin, D., Yekutieli, D., Gershoni, J. M., & Pupko, T. (2007) · Molecular Immunology · doi:10.1016/j.molimm.2007.10.016 · Cited by 251 · see citing works
Gilman, M. S. A., Castellanos, C. A., Chen, M., Ngwuta, J. O., Goodwin, E. C., Moin, S. M., Más, V., Melero, J. A., Wright, P. F., Graham, B. S., et al. (2016) · Science Immunology · doi:10.1126/sciimmunol.aaj1879 · Cited by 239 · see citing works
Self-citationWest, A. P., Diskin, R., Nussenzweig, M. C., & Björkman, P. J. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208984109 · Cited by 231 · see citing works
Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold
Azoitei, M. L., Correia, B. E., Ban, Y.-E. A., Carrico, C., Kalyuzhniy, O., Chen, L., Schroeter, A., Huang, P.-S., McLellan, J. S., Kwong, P. D., et al. (2011) · Science · doi:10.1126/science.1209368 · Cited by 224 · see citing works
Self-citationCorreia, B. E., Ban, Y. A., Holmes, M. A., Xu, H., Ellingson, K., Kraft, Z., Carrico, C., Boni, E., Sather, D. N., Zenobia, C., et al. (2010) · Structure · doi:10.1016/j.str.2010.06.010 · Cited by 213 · see citing works
Self-citationIterative structure-based improvement of a fusion-glycoprotein vaccine against RSV
Joyce, M. G., Zhang, B., Ou, L., Chen, M., Chuang, G., Druz, A., Kong, W., Lai, Y., Rundlet, E. J., Tsybovsky, Y., et al. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3267 · Cited by 168 · see citing works
De novo protein design: how do we expand into the universe of possible protein structures?
Woolfson, D. N., Bartlett, G. J., Burton, A. J., Heal, J. W., Niitsu, A., Thomson, A. R., & Wood, C. W. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.05.009 · Cited by 155 · see citing works
A ‘periodic table’ for protein structures
Taylor, W. R. (2002) · Nature · doi:10.1038/416657a · Cited by 153 · see citing works
Packing of apolar side chains enables accurate design of highly stable membrane proteins
Mravic, M., Thomaston, J. L., Tucker, M. R., Solomon, P. E., Liu, L., & DeGrado, W. F. (2019) · Science · doi:10.1126/science.aav7541 · Cited by 133 · see citing works
What Are the Most Powerful Immunogen Design Vaccine Strategies?Preprint
Burton, D. R. (2017) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a030262 · Cited by 132 · see citing works
Procko, E., Berguig, G. Y., Shen, B. W., Song, Y., Frayo, S., Convertine, A. J., Margineantu, D., Booth, G., Correia, B. E., Cheng, Y., et al. (2014) · Cell · doi:10.1016/j.cell.2014.04.034 · Cited by 127 · see citing works
Self-citationMcLellan, J. S., Chen, M., Chang, J., Yang, Y., Kim, A., Graham, B. S., & Kwong, P. D. (2010) · Journal of Virology · doi:10.1128/jvi.01579-10 · Cited by 127 · see citing works
Avnir, Y., Tallarico, A. S. C., Zhu, Q. K., Bennett, A. S., Connelly, G., Sheehan, J., Sui, J., Fahmy, A., Huang, C., Cadwell, G., et al. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004103 · Cited by 127 · see citing works
Principles for designing proteins with cavities formed by curved β sheets
Marcos, E., Basanta, B., Chidyausiku, T. M., Tang, Y., Oberdorfer, G., Liu, G., Swapna, G. V. T., Guan, R., Silva, D., Dou, J., et al. (2017) · Science · doi:10.1126/science.aah7389 · Cited by 127 · see citing works
High-resolution design of a protein loop
Hu, X., Wang, H., Ke, H., & Kuhlman, B. A. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707977104 · Cited by 126 · see citing works
Strauch, E.-M., Bernard, S. M., La, D., Bohn, A. J., Lee, P. S., Anderson, C. E., Nieusma, T., Holstein, C. A., Garcia, N. K., Hooper, K. A., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3907 · Cited by 119 · see citing works
Anatomy of β-Strands at Protein–Protein Interfaces
Watkins, A. M., & Arora, P. S. (2014) · ACS Chemical Biology · doi:10.1021/cb500241y · Cited by 117 · see citing works
West, A. P., Diskin, R., Nussenzweig, M. C., & Björkman, P. J. (2012) · Retrovirology · doi:10.1186/1742-4690-9-s2-o33 · Cited by 114 · see citing works
McLellan, J. S., Correia, B. E., Chen, M., Yang, Y., Graham, B. S., Schief, W. R., & Kwong, P. D. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.04.044 · Cited by 105 · see citing works
Self-citationRapid search for tertiary fragments reveals protein sequence–structure relationships
Zhou, J., & Grigoryan, G. (2014) · Protein Science · doi:10.1002/pro.2610 · Cited by 105 · see citing works
Heads, stalks and everything else: how can antibodies eradicate influenza as a human disease?
Neu, K. E., Henry, C., & Wilson, P. C. (2016) · Current Opinion in Immunology · doi:10.1016/j.coi.2016.05.012 · Cited by 87 · see citing works
Isolation of antibody V(D)J sequences from single cell sorted rhesus macaque B cells
Sundling, C., Phad, G. E., Douagi, I., Navis, M., & Hedestam, G. B. K. (2012) · Journal of Immunological Methods · doi:10.1016/j.jim.2012.09.003 · Cited by 78 · see citing works
Más, V., Laura, R., Olmedillas, E., Cano, O., Palomo, C., Terrón, M. C., Luque, D., Melero, J. A., & McLellan, J. S. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005859 · Cited by 78 · see citing works
Self-citationFenton, C., Scott, L. J., & Plosker, G. L. (2004) · Pediatric Drugs · doi:10.2165/00148581-200406030-00004 · Cited by 75 · see citing works
Tian, D., Battles, M. B., Moin, S. M., Chen, M., Modjarrad, K., Kumar, A., Kanekiyo, M., Graepel, K. W., Taher, N. M., Hotard, A. L., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01858-w · Cited by 71 · see citing works
Towards functional de novo designed proteins
Dawson, W., Rhys, G. G., & Woolfson, D. N. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.06.011 · Cited by 69 · see citing works
Finucane, M. D., Tuna, M., Lees, J. H., & Woolfson, D. N. (1999) · Biochemistry · doi:10.1021/bi990765n · Cited by 67 · see citing works
Human antibody recognition of antigenic site IV on Pneumovirus fusion proteins
Mousa, J. J., Binshtein, E., Human, S., Fong, R. H., Alvarado, G. S., Doranz, B. J., Moore, M. L., Ohi, M. D., & Crowe, J. E. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1006837 · Cited by 44 · see citing works
Rosetta FunFolDes – A general framework for the computational design of functional proteins
Bonet, J., Wehrle, S., Schriever, K., Yang, C., Billet, A., Sesterhenn, F., Scheck, A., Sverrisson, F., Veselková, B., Vollers, S. S., et al. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006623 · Cited by 41 · see citing works
Self-citationHolliday, G., Fischer, J. D., Mitchell, J. B. O., & Thornton, J. (2011) · The FEBS Journal · doi:10.1111/j.1742-4658.2011.08190.x · Cited by 39 · see citing works
Sesterhenn, F., Galloux, M., Vollers, S. S., Csepregi, L., Yang, C., Descamps, D., Bonet, J., Friedensohn, S., Gaínza, P., Corthésy, P., et al. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000164 · Cited by 35 · see citing works
Self-citationGottstein, D., Kirchner, D. K., & Güntert, P. (2012) · Journal of Biomolecular NMR · doi:10.1007/s10858-012-9615-8 · Cited by 32 · see citing works
Wang, Y., Sundling, C., Wilson, R., O'Dell, S. J., Chen, Y., Dai, K., Phad, G. E., Zhu, J., Xiao, Y., Mascola, J. R., et al. (2016) · The Journal of Immunology · doi:10.4049/jimmunol.1502543 · Cited by 28 · see citing works
Self-citationStructure-based immunogen design — leading the way to the new age of precision vaccines
Sesterhenn, F., Bonet, J., & Correia, B. E. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.06.002 · Cited by 27 · see citing works
Self-citationBonet, J., Segura, J., Planas-Iglesias, J., Oliva, B., & Fernández‐Fuentes, N. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu129 · Cited by 20 · see citing works
Self-citationZhang, R., Martinez, D. R., Nguyen, Q. N., Pollara, J., Arifin, T., Stolarchuk, C., Foulger, A., Amos, J. D., Parks, R., Himes, J. E., et al. (2016) · Nature Communications · doi:10.1038/ncomms12131 · Cited by 16 · see citing works
Wang, Y., O'Dell, S. J., Turner, H. L., Chiang, C.-I., Lei, L., Guenaga, J., Wilson, R., Martinez-Murillo, P., Doria‐Rose, N. A., Ward, A. B., et al. (2017) · Journal of Virology · doi:10.1128/jvi.00910-17 · Cited by 14 · see citing works
Self-citationChimeric Pneumoviridae fusion proteins as immunogens to induce cross‐neutralizing antibody responses
Olmedillas, E., Cano, O., Martínez, I., Luque, D., Terrón, M. C., McLellan, J. S., Melero, J. A., & Más, V. (2017) · EMBO Molecular Medicine · doi:10.15252/emmm.201708078 · Cited by 14 · see citing works
Self-citationBonet, J., Harteveld, Z., Sesterhenn, F., Scheck, A., & Correia, B. E. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2796-3 · Cited by 14 · see citing works
Self-citationLPDI-EPFL/trivalent_cocktail: RSV_trivalent_cocktail
Sesterhenn, F. (2020) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.3724330 · Cited by 1 · see citing works
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Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., et al. (2022) · doi:10.1101/2022.12.09.519842 · Cited by 2,369 · see citing works
De novo design of protein structure and function with RFdiffusion
Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., et al. (2023) · Nature · doi:10.1038/s41586-023-06415-8 · Cited by 2,325 · see citing works
Scaffolding protein functional sites using deep learning
Wang, J., Lisanza, S., Juergens, D., Tischer, D., Watson, J. L., Castro, K. M., Ragotte, R., Saragovi, A., Milles, L. F., Baek, M., et al. (2022) · Science · doi:10.1126/science.abn2100 · Cited by 487 · see citing works
Self-citationBroad betacoronavirus neutralization by a stem helix–specific human antibody
Pinto, D., Sauer, M. M., Czudnochowski, N., Low, J. S., Tortorici, M. A., Housley, M. P., Noack, J., Walls, A. C., Bowen, J. E., Guarino, B., et al. (2021) · Science · doi:10.1126/science.abj3321 · Cited by 381 · see citing works
Antibodies to combat viral infections: development strategies and progress
Pantaleo, G., Correia, B. E., Fenwick, C. W., Joo, V., & Perez, L. H. (2022) · Nature Reviews Drug Discovery · doi:10.1038/s41573-022-00495-3 · Cited by 286 · see citing works
Self-citationMachine learning for functional protein design
Notin, P., Rollins, N. J., Gal, Y., Sander, C., & Marks, D. S. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02127-0 · Cited by 278 · see citing works
De novo design of protein interactions with learned surface fingerprints
Gaínza, P., Wehrle, S., Hall‐Beauvais, A. V., Marchand, A., Scheck, A., Harteveld, Z., Buckley, S., Ni, D., Tan, S., Sverrisson, F., et al. (2023) · Nature · doi:10.1038/s41586-023-05993-x · Cited by 241 · see citing works
Self-citationDe novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2
Linsky, T. W., Vergara, R., Codina, N., Nelson, J. W., Walker, M. J., Su, W., Barnes, C. O., Hsiang, T.-Y., Esser-Nobis, K., Yu, K., et al. (2020) · Science · doi:10.1126/science.abe0075 · Cited by 216 · see citing works
Structural basis for broad coronavirus neutralization
Sauer, M. M., Tortorici, M. A., Park, Y., Walls, A. C., Homad, L. J., Acton, O. J., Bowen, J. E., Wang, C., Xiong, X., de van der Schueren, W., et al. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00596-4 · Cited by 174 · see citing works
Opportunities and challenges in design and optimization of protein function
Listov, D., Goverde, C. A., Correia, B. E., & Fleishman, S. J. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00718-y · Cited by 192 · see citing works
Self-citationRahban, M., Zolghadri, S., Salehi, N., Ahmad, F., Haertlé, T., Rezaei‐Ghaleh, N., Sawyer, L., & Saboury, A. A. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.06.154 · Cited by 172 · see citing works
A Brief History of De Novo Protein Design: Minimal, Rational, and Computational
Woolfson, D. N. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167160 · Cited by 162 · see citing works
Game changers in science and technology - now and beyond
Betz, U. A. K., Arora, L., Assal, R. A., de Azevedo, H. F. Z., Baldwin, J., Becker, M. S., Bostock, S., Cheng, V. W. T., Egle, T., Ferrari, N., et al. (2023) · Technological Forecasting and Social Change · doi:10.1016/j.techfore.2023.122588 · Cited by 146 · see citing works
Integrated biotechnological and AI innovations for crop improvement
Li, G., An, L., Yang, W., Yang, L., Wei, T., Shi, J., Wang, J., Doonan, J. H., Xie, K., Fernie, A. R., et al. (2025) · Nature · doi:10.1038/s41586-025-09122-8 · Cited by 145 · see citing works
Deep learning techniques have significantly impacted protein structure prediction and protein design
Pearce, R., & Zhang, Y. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.01.007 · Cited by 127 · see citing works
Sparks of function by de novo protein design
Chu, A. E., Lu, T., & Huang, P. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02133-2 · Cited by 117 · see citing works
Mining of epitopes on spike protein of SARS-CoV-2 from COVID-19 patients
Zhang, B., Hu, Y., Chen, L., Yau, T. C. C., Tong, Y., Hu, J., Cai, J., Chan, K., Dou, Y., Deng, J., et al. (2020) · Cell Research · doi:10.1038/s41422-020-0366-x · Cited by 114 · see citing works
A new age in protein design empowered by deep learning
Khakzad, H., Igashov, I., Schneuing, A., Goverde, C. A., Bronstein, M. M., & Correia, B. E. (2023) · Cell Systems · doi:10.1016/j.cels.2023.10.006 · Cited by 113 · see citing works
Self-citationImmunopathology of RSV: An Updated Review
Bergeron, H. C., & Tripp, R. A. (2021) · Viruses · doi:10.3390/v13122478 · Cited by 109 · see citing works
De novo protein design by inversion of the <scp>AlphaFold</scp> structure prediction network
Goverde, C. A., Wolf, B., Khakzad, H., Rosset, S., & Correia, B. E. (2023) · Protein Science · doi:10.1002/pro.4653 · Cited by 103 · see citing works
Self-citationBottom-up de novo design of functional proteins with complex structural features
Yang, C., Sesterhenn, F., Bonet, J., van Aalen, E. A., Scheller, L., Abriata, L. A., Cramer, J. T., Wen, X., Rosset, S., Georgeon, S., et al. (2021) · Nature Chemical Biology · doi:10.1038/s41589-020-00699-x · Cited by 84 · see citing works
Self-citationProtein engineering design from directed evolution to de novo synthesis
Xiong, W., Liu, B., Shen, Y., Jing, K., & Savage, T. (2021) · Biochemical Engineering Journal · doi:10.1016/j.bej.2021.108096 · Cited by 94 · see citing works
Engineering Self-Assembling Protein Nanoparticles for Therapeutic Delivery
Olshefsky, A., Richardson, C., Pun, S. H., & King, N. P. (2022) · Bioconjugate Chemistry · doi:10.1021/acs.bioconjchem.2c00030 · Cited by 91 · see citing works
Protective neutralizing antibodies from human survivors of Crimean-Congo hemorrhagic fever
Fels, J. M., Maurer, D. P., Herbert, A. S., Wirchnianski, A. S., Vergnolle, O., Cross, R. W., Abelson, D. M., Moyer, C. L., Mishra, A. K., Aguilan, J. T., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.001 · Cited by 87 · see citing works
Point-of-Care Diagnostics of COVID-19: From Current Work to Future Perspectives
Hussein, H. A., Hassan, R. Y. A., Chino, M., & Febbraio, F. (2020) · Sensors · doi:10.3390/s20154289 · Cited by 89 · see citing works
Computer-aided understanding and engineering of enzymatic selectivity
Wu, L., Qin, L., Nie, Y., Xu, Y., & Zhao, Y. (2021) · Biotechnology Advances · doi:10.1016/j.biotechadv.2021.107793 · Cited by 80 · see citing works
Guarra, F., & Colombo, G. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00513 · Cited by 79 · see citing works
Rapidly determining the 3D structure of proteins by surface-enhanced Raman spectroscopy
Ma, H., Yan, S., Lu, X., Bao, Y., Liu, J., Liao, L., Dai, K., Cao, M., Zhao, X., Yan, H., et al. (2023) · Science Advances · doi:10.1126/sciadv.adh8362 · Cited by 75 · see citing works
Protein design via deep learning
Ding, W., Nakai, K., & Gong, H. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac102 · Cited by 66 · see citing works
Protein engineering strategies for rational immunogen design
Caradonna, T. M., & Schmidt, A. G. (2021) · npj Vaccines · doi:10.1038/s41541-021-00417-1 · Cited by 68 · see citing works
Enabling technology and core theory of synthetic biology
Zhang, X., Liu, C., Dai, J., Yuan, Y., Gao, C., Feng, Y. F., Wu, B., Wei, P., You, C., Wang, X., et al. (2023) · Science China Life Sciences · doi:10.1007/s11427-022-2214-2 · Cited by 65 · see citing works
Marchand, A., Hall‐Beauvais, A. V., & Correia, B. E. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102370 · Cited by 65 · see citing works
Self-citationGattinger, P., Niespodziana, K., Stiasny, K., Sahanic, S., Tulaeva, I., Borochova, K., Dorofeeva, Y., Schlederer, T., Sonnweber, T., Höfer, G., et al. (2021) · Allergy · doi:10.1111/all.15066 · Cited by 64 · see citing works
Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response
Dickey, T. H., Tang, W. K., Butler, B., Ouahes, T., Orr-Gonzalez, S., Salinas, N. D., Lambert, L., & Tolia, N. H. (2022) · Science Advances · doi:10.1126/sciadv.abq8276 · Cited by 60 · see citing works
Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design
Schoeder, C. T., Schmitz, S., Adolf‐Bryfogle, J., Sevy, A. M., Finn, J. A., Sauer, M. F., Bozhanova, N. G., Mueller, B. K., Sangha, A. K., Bonet, J., et al. (2021) · Biochemistry · doi:10.1021/acs.biochem.0c00912 · Cited by 57 · see citing works
Self-citationKudlacek, S. T., Metz, S., Thiono, D., Payne, A. M., Phan, T. T. N., Tian, S., Forsberg, L. J., Maguire, J. B., Seim, I., Zhang, S., et al. (2021) · Science Advances · doi:10.1126/sciadv.abg4084 · Cited by 57 · see citing works
Vaccination induces broadly neutralizing antibody precursors to HIV gp41
Schiffner, T., Phung, I., Ray, R., Irimia, A., Tian, M., Swanson, O. M., Lee, J. H., Lee, C.-C. D., Marina-Zárate, E., Cho, S. Y., et al. (2024) · Nature Immunology · doi:10.1038/s41590-024-01833-w · Cited by 56 · see citing works
Self-citationBringing immunofocusing into focus
Musunuri, S., Weidenbacher, P. A. B., & Kim, P. S. (2024) · npj Vaccines · doi:10.1038/s41541-023-00792-x · Cited by 48 · see citing works
The Status and Prospects of Epstein–Barr Virus Prophylactic Vaccine Development
Sun, C., Chen, X., Kang, Y., & Zeng, M. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.677027 · Cited by 52 · see citing works
Heterotypic interactions drive antibody synergy against a malaria vaccine candidate
Ragotte, R. J., Pulido, D., Lias, A. M., Quinkert, D., Alanine, D. G. W., Jamwal, A., Davies, H. D., Nacer, A., Lowe, E. D., Grime, G. W., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28601-4 · Cited by 47 · see citing works
Structural basis for respiratory syncytial virus and human metapneumovirus neutralization
Miller, R. J., & Mousa, J. J. (2023) · Current Opinion in Virology · doi:10.1016/j.coviro.2023.101337 · Cited by 46 · see citing works
In silico evolution of autoinhibitory domains for a PD-L1 antagonist using deep learning models
Goudy, O. J., Nallathambi, A., Kinjo, T., Randolph, N. Z., & Kuhlman, B. A. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2307371120 · Cited by 46 · see citing works
Can We AlphaFold Our Way Out of the Next Pandemic?
Higgins, M. K. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167093 · Cited by 46 · see citing works
SARS-COV-2, infection, transmission, transcription, translation, proteins, and treatment: A review
Emrani, J., Ahmed, M., Jeffers-Francis, L. K., Teleha, J. C., Mowa, C. N., Newman, R. H., & Thomas, M. D. (2021) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2021.10.172 · Cited by 46 · see citing works
Non-human primate models of human respiratory infections
Lemaître, J., Naninck, T., Delache, B., Creppy, J., Huber, P., Holzapfel, M., Bouillier, C., Contreras, V., Martinon, F., Kahlaoui, N., et al. (2021) · Molecular Immunology · doi:10.1016/j.molimm.2021.04.010 · Cited by 45 · see citing works
SEMA 2.0: web-platform for B-cell conformational epitopes prediction using artificial intelligence
Ivanisenko, N. V., Shashkova, T., Shevtsov, A., Sindeeva, M., Umerenkov, D., & Kardymon, O. L. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae386 · Cited by 47 · see citing works
Antibody-guided structure-based vaccines
Kwong, P. D., DeKosky, B. J., & Ulmer, J. B. (2020) · Seminars in Immunology · doi:10.1016/j.smim.2020.101428 · Cited by 43 · see citing works
Multilayer Genetic Circuits for Dynamic Regulation of Metabolic Pathways
Cui, S., Lv, X., Xu, X., Chen, T., Zhang, H., Liu, Y., Li, J., Du, G., Ledesma‐Amaro, R., & Liu, L. (2021) · ACS Synthetic Biology · doi:10.1021/acssynbio.1c00073 · Cited by 42 · see citing works
Amcheslavsky, A., Wallace, A., Ejemel, M., Li, Q., McMahon, C. T., Stoppato, M., Giuntini, S., Schiller, Z. A., Pondish, J. R., Toomey, J. R., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-81895-0 · Cited by 36 · see citing works
Self-citationWang, J., Watson, J. L., & Lisanza, S. L. (2024) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a041472 · Cited by 36 · see citing works
Interleukin-2 superkines by computational design
Ren, J., Chu, A. E., Jude, K. M., Picton, L. K., Kare, A. J., Su, L., Romero, A. M., Huang, P., & García, K. C. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2117401119 · Cited by 35 · see citing works
Exploration of novel αβ-protein folds through de novo design
Minami, S., Kobayashi, N., Sugiki, T., Nagashima, T., Fujiwara, T., Koga, R., Chikenji, G., & Koga, N. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01029-0 · Cited by 34 · see citing works
Systematic identification of structure-specific protein–protein interactions
(2024) · doi:10.1038/s44320-024-00037-6 · Cited by 34 · see citing works
Self-citationCurrent progress and challenges in the design and development of a successful COVID-19 vaccine
Li, T.-T., Zhang, T.-Y., Gu, Y., Li, S., & Xia, N. (2021) · Fundamental Research · doi:10.1016/j.fmre.2021.01.011 · Cited by 25 · see citing works
Enlightening Allostery: Designing Switchable Proteins by Photoreceptor Fusion
Mathony, J., & Niopek, D. (2020) · Advanced Biology · doi:10.1002/adbi.202000181 · Cited by 29 · see citing works
Ivanochko, D., Fabra-García, A., Teelen, K., van de Vegte‐Bolmer, M., van Gemert, G., Newton, J. C., Semesi, A., de Bruijni, M. H. C., Bolscher, J. M., Ramjith, J., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.01.013 · Cited by 28 · see citing works
Self-citationVaccine design and development: Exploring the interface with computational biology and AI
Ananya, A., Panchariya, D. C., Karthic, A., Singh, S. P., Mani, A., Chawade, A., & Kushwaha, S. K. (2024) · International Reviews of Immunology · doi:10.1080/08830185.2024.2374546 · Cited by 27 · see citing works
Design of complicated all-α protein structures
Sakuma, K., Kobayashi, N., Sugiki, T., Nagashima, T., Fujiwara, T., Suzuki, K., Kobayashi, N., Murata, T., Kosugi, T., Tatsumi-Koga, R., et al. (2021) · bioRxiv · doi:10.1038/s41594-023-01147-9 · Cited by 19 · see citing works
Implementation of a controlled human infection model for evaluation of HCV vaccine candidates
Barnes, E. J., Cooke, G., Lauer, G. M., & Chung, R. T. (2022) · Hepatology · doi:10.1002/hep.32632 · Cited by 26 · see citing works
Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein
Adhikari, P., & Ching, W. Y. (2020) · RSC Advances · doi:10.1039/d0ra08222h · Cited by 25 · see citing works
Engineered Repeat Protein Hybrids: The New Horizon for Biologic Medicines and Diagnostic Tools
Uribe, K. B., Guisasola, E., Aires, A., López‐Martínez, E., Guedes, G., Sasselli, I. R., & Cortajarena, A. L. (2021) · Accounts of Chemical Research · doi:10.1021/acs.accounts.1c00440 · Cited by 25 · see citing works
Subdominance in Antibody Responses: Implications for Vaccine Development
Lindahl, G. (2020) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00078-20 · Cited by 21 · see citing works
De, R., Song, Y. H., Mahata, M. K., & Lee, K. T. (2022) · Journal of Materials Chemistry B · doi:10.1039/d2tb00246a · Cited by 24 · see citing works
Liu, X., Wang, S., Sun, Y., Liao, Y., Jiang, G., Sun, B., Yu, J., & Zhao, D. (2025) · EBioMedicine · doi:10.1016/j.ebiom.2025.105638 · Cited by 24 · see citing works
Computational design of vaccine immunogens
Castro, K. M., Scheck, A., Xiao, S., & Correia, B. E. (2022) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2022.102821 · Cited by 22 · see citing works
Self-citationFlu Universal Vaccines: New Tricks on an Old Virus
Du, R., Cui, Q., & Rong, L. (2020) · Virologica Sinica · doi:10.1007/s12250-020-00283-6 · Cited by 22 · see citing works
The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes
Lipsh‐Sokolik, R., Listov, D., & Fleishman, S. J. (2020) · Protein Science · doi:10.1002/pro.3970 · Cited by 20 · see citing works
Virus-like Particle Vaccines: A Prospective Panacea Against an Avian Influenza Panzootic
Ninyio, N. N., Ho, K. L., Omar, A. R., Tan, W. S., Iqbal, M., & Mariatulqabtiah, A. R. (2020) · Vaccines · doi:10.3390/vaccines8040694 · Cited by 21 · see citing works
An epitope-specific chemically defined nanoparticle vaccine for respiratory syncytial virus
Zúñiga, A., Rassek, O., Vrohlings, M., Marrero, A., Moehle, K., Robinson, J. A., & Ghasparian, A. (2021) · npj Vaccines · doi:10.1038/s41541-021-00347-y · Cited by 21 · see citing works
A generic framework for hierarchical de novo protein design
Harteveld, Z., Bonet, J., Rosset, S., Yang, C., Sesterhenn, F., & Correia, B. E. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2206111119 · Cited by 21 · see citing works
Self-citationEpitope-focused immunogen design based on the ebolavirus glycoprotein HR2-MPER region
Schoeder, C. T., Gilchuk, P., Sangha, A. K., Ledwitch, K. V., Malherbe, D. C., Zhang, X., Binshtein, E., Williamson, L. E., Martina, C. E., Dong, J., et al. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010518 · Cited by 20 · see citing works
Principles and Methods in Computational Membrane Protein Design
Vorobieva, A. A. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167154 · Cited by 20 · see citing works
Is Novelty Predictable?Preprint
Fannjiang, C., & Listgarten, J. (2023) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a041469 · Cited by 19 · see citing works
Bizot, E., Sulla, V. P., Vauloup‐Fellous, C., Rameix‐Welti, M., Gajdos, V., & Seddiki, N. (2025) · Pediatric Allergy and Immunology · doi:10.1111/pai.70257 · Cited by 19 · see citing works
Self-citationRecent Progress Using De Novo Design to Study Protein Structure, Design and Binding Interactions
Ferrando, J., & Solomon, L. A. (2021) · Life · doi:10.3390/life11030225 · Cited by 19 · see citing works
Bacteriophage protein PEIP is a potent Bacillus subtilis enolase inhibitor
Zhang, K., Li, S., Wang, Z., Wang, Z., Mulvenna, N., Yang, H., Zhang, P., Chen, H., Li, Y., Wang, H., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111026 · Cited by 18 · see citing works
Self-citationAn epitope-enriched immunogen expands responses to a conserved viral site
Caradonna, T. M., Ronsard, L., Yousif, A. S., Windsor, I. W., Hecht, R., Moreno, T. B., Roffler, A. A., Maron, M. J., Maurer, D. P., Feldman, J. E., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111628 · Cited by 18 · see citing works
Computational Methods in Immunoinformatics: Epitope Discovery and Diagnostic Applications
Bulla, A. C. S., da Silva, A. S., Sereno, B. P., Dias, M. F. R., & da Silva, M. L. (2025) · ACS Omega · doi:10.1021/acsomega.5c05538 · Cited by 17 · see citing works
Gräwe, A., & Merkx, M. (2022) · ACS Sensors · doi:10.1021/acssensors.2c01726 · Cited by 17 · see citing works
Toward complete rational control over protein structure and function through computational design
Adolf‐Bryfogle, J., Teets, F. D., & Bahl, C. D. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.10.015 · Cited by 17 · see citing works
Advancing sustainable biotechnology through protein engineering
Bergeson, A. R., & Alper, H. S. (2024) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2024.07.006 · Cited by 17 · see citing works
De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design
Chu, A. E., Fernández, D., Liu, J., Eguchi, R. R., & Huang, P. (2022) · BioDesign Research · doi:10.34133/2022/9842315 · Cited by 13 · see citing works
Structural Virology: The Key Determinants in Development of Antiviral Therapeutics
Handa, T., Saha, A., Narayanan, A., Ronzier, E., Kumar, P., Singla, J., & Tomar, S. (2025) · Viruses · doi:10.3390/v17030417 · Cited by 15 · see citing works
A Pan-Pneumovirus vaccine based on immunodominant epitopes of the fusion protein
Huang, J., Miller, R. J., & Mousa, J. J. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.941865 · Cited by 14 · see citing works
GDockScore: a graph-based protein–protein docking scoring function
McFee, M. C., & Kim, P. M. (2023) · Bioinformatics Advances · doi:10.1093/bioadv/vbad072 · Cited by 14 · see citing works
Dai, L., Song, J. G., Xu, L., Gao, Z., Xu, S., Chai, Y., Wang, L., Yang, M. Y., Ma, T., Wang, Q., et al. (2023) · hLife · doi:10.1016/j.hlife.2023.09.003 · Cited by 14 · see citing works
Breakthroughs in computational design methods open up new frontiers for de novo protein engineering
Meinen, B. A., & Bahl, C. D. (2021) · Protein Engineering Design and Selection · doi:10.1093/protein/gzab007 · Cited by 14 · see citing works
Targeting Viral Surface Proteins through Structure-Based Design
Narkhede, Y. B., Gonzalez, K. J., & Strauch, E. (2021) · Viruses · doi:10.3390/v13071320 · Cited by 14 · see citing works
Pinto, D., Sauer, M. M., Czudnochowski, N., Low, J. S., Tortorici, M. A., Housley, M. P., Noack, J., Walls, A. C., Bowen, J. E., Guarino, B., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.09.442808 · Cited by 15 · see citing works
Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity
Cano‐Muñoz, M., Polo-Megías, D., Cámara-Artigas, A., Gavira, J. A., López-Rodríguez, M. J., Laumond, G., Schmidt, S., Demiselle, J., Bahram, S., Moog, C., et al. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.10.031 · Cited by 13 · see citing works
Application of Predictive Analytics in Agriculture
Gupta, S. K. (2022) · TechnoareteTransactions on Intelligent Data Mining and Knowledge Discovery · doi:10.36647/ttidmkd/02.04.a001 · Cited by 13 · see citing works
Harrison, T. E., Alam, N., Farrell, B., Quinkert, D., Lias, A. M., King, L. D. W., Barfod, L. K., Draper, S. J., Campeotto, I., & Higgins, M. K. (2024) · EMBO Molecular Medicine · doi:10.1038/s44321-024-00123-0 · Cited by 12 · see citing works
End-to-End deep structure generative model for protein designPreprint
Lai, B., McPartlon, M., & Xu, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.09.499440 · Cited by 12 · see citing works
DE-STRESS: a user-friendly web application for the evaluation of protein designs
Stam, M. J., & Wood, C. W. (2021) · Protein Engineering Design and Selection · doi:10.1093/protein/gzab029 · Cited by 11 · see citing works
Efficient protein structure generation with sparse denoising models
Jendrusch, M., & Korbel, J. O. (2025) · Nature Machine Intelligence · doi:10.1038/s42256-025-01100-z · Cited by 10 · see citing works
What Can De Novo Protein Design Bring to the Treatment of Hematological Disorders?
Lu, H. J., Cheng, Z., Hu, Y., & Tang, L. V. (2023) · Biology · doi:10.3390/biology12020166 · Cited by 10 · see citing works
Jacque, É., Chottin, C., Laubreton, D., Nogré, M., Ferret, C., de Marcos, S., Baptista, L., Drajac, C., Mondon, P., de Romeuf, C., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.683902 · Cited by 10 · see citing works
Self-citationKretschmer, S., & Kortemme, T. (2022) · Proceedings of the IEEE · doi:10.1109/jproc.2022.3157898 · Cited by 10 · see citing works
Nagarathinam, K., Scheck, A., Labuhn, M., Stroh, L. J., Herold, E., Veselková, B., Tune, S., Cramer, J., Rosset, S., Vollers, S. S., et al. (2024) · Science Advances · doi:10.1126/sciadv.ado2600 · Cited by 9 · see citing works
Self-citationHuang, Q.-L., Lang, Q., Li, Y., Wang, F., Han, X., Luo, L., Duan, X., Cao, X., Wang, Y., Bai, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-63084-z · Cited by 9 · see citing works
Self-citation
- Authors
- Sesterhenn, F., Yang, C., Bonet, J., Cramer, J. T., Wen, X., Wang, Y., Chiang, C.-I., Abriata, L. A., Kucharska, I., Castoro, G., Vollers, S. S., Galloux, M., Dheilly, E., Rosset, S., Corthésy, P., Georgeon, S., Villard, M., Richard, C.-A., Descamps, D., Delgado, T., Oricchio, E., Rameix-Welti, M.-A., Más, V., Ervin, S., Eléouët, J.-F., Riffault, S., Bates, J. T., Julien, J.-P., Li, Y., Jardetzky, T., Krey, T., & Correia, B. E.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- Medizinische Hochschule Hannover (DE)
- Stanford Medicine (US)
- Institute for Bioscience and Biotechnology Research (US)
- University of Toronto (CA)
- Université de Versailles Saint-Quentin-en-Yvelines (FR)
- École Polytechnique Fédérale de Lausanne (CH)
- Instituto de Salud Carlos III (ES)
- UMR1173, INSERM, Université de Versailles St. Quentin, 78180 Montigny le Bretonneux, France.
- Atrium Health Wake Forest Baptist (US)
- University of Mississippi Medical Center (US)
- University of Maryland, Baltimore (US)
- Corresponding author
- Sesterhenn, Fabian
- Yang, Che
- Bonet, Jaume
- Cramer, Johannes T.
- Correia, Bruno E.
- ORCID
- Sesterhenn, Fabian
- Yang, Che
- Bonet, Jaume
- Cramer, Johannes T.
- Wen, Xiaolin
- Wang, Yimeng
- Chiang, Chi-I
- Abriata, Luciano A.
- Kucharska, Iga
- Vollers, Sabrina S.
- Galloux, Marie
- Rosset, Stéphane
- Georgeon, Sandrine
- Villard, Mélanie
- Richard, Charles-Adrien
- Descamps, Delphyne
- Oricchio, Elisa
- Rameix-Welti, Marie-Anne
- Más, Vicente
- Ervin, Sean
- Eléouët, Jean-François
- Riffault, Sabine
- Bates, John T.
- Julien, Jean-Philippe
- Li, Yuxing
- Jardetzky, Theodore
- Krey, Thomas
- Correia, Bruno E.
- Venue
- Science
- Published
- 2020-05-15
- Volume
- 368
- Issue
- 6492
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7391827
- OpenAlex
- W3024848554
- Cited by
- 191
- References
- 85
- Citations by year
- 2026: 19 · 2025: 20 · 2024: 30 · 2023: 26 · 2022: 35 · 2021: 44 · 2020: 17
- FWCI
- 9.90
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- RePEc: Research Papers in Economics (submittedVersion)
- HAL (submittedVersion, other-oa)
- DORA PSI (Paul Scherrer Institute) (submittedVersion)
- Funders
- European Research Council (716058)
- Swiss National Science Foundation (310030_163139)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Keywords
- de novo protein design, respiratory syncytial virus, neutralizing antibodies, vaccine design, non-human primates, therapeutic antibodies
- MeSH terms
- Humans, Protein Conformation, Recombinant Fusion Proteins, Protein Engineering, Immunodominant Epitopes, Respiratory Syncytial Virus, Human, Computational Biology, Amino Acid Motifs, Respiratory Syncytial Virus Vaccines, Antibodies, Neutralizing, Single-Domain Antibodies
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