Massively parallel de novo protein design for targeted therapeutics

Cited by (457)

Items 101–200 of 457

1. De novo coiled-coil peptides as scaffolds for disrupting protein–protein interactions
   Jordan M. Fletcher, Katherine A. Horner, Gail J. Bartlett, Guto G. Rhys, Andrew John Wilson, Derek N. Woolfson · 2018 · Chemical Science
2. Context-aware geometric deep learning for protein sequence design
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3. The stability and dynamics of computationally designed proteins
   Natali A. Gonzalez, Brigitte A Li, Michelle E. McCully · 2022 · Protein Engineering Design and Selection
4. Recurring and Adaptable Binding Motifs in Broadly Neutralizing Antibodies to Influenza Virus Are Encoded on the D3-9 Segment of the Ig Gene
   Nicholas C. Wu, Seiya Yamayoshi, Mutsumi Ito, Ryuta Uraki, Yoshihiro Kawaoka, Ian A. Wilson · 2018 · Cell Host & Microbe
5. Deep scanning lysine metabolism in Escherichia coli
   Marcelo C. Bassalo, Andrew D. Garst, Alaksh Choudhury, William C Grau, Eun Joong Oh, Eileen C. Spindler, Tanya Warnecke Lipscomb, Ryan T. Gill · 2018 · Molecular Systems Biology
6. The Central Dogma revisited: Insights from protein synthesis, CRISPR, and beyond
   Alexander M. Ille, Hannah Lamont, Michael B. Mathews · 2022 · Wiley Interdisciplinary Reviews - RNA
7. Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization
   Jiaqi Li, Guangbo Kang, Jiewen Wang, Haibin Yuan, Yili Wu, Shuxian Meng, Ping Wang, Miao Zhang, Yuli Wang, Yuanhang Feng et al. · 2023 · International Journal of Biological Macromolecules
8. Directed Disulfide Pairing and Folding of Peptides for the De Novo Development of Multicyclic Peptide Libraries
   Shuaimin Lu, Yapei Wu, Jinjing Li, Xiaoting Meng, Chenliang Hu, Yibing Zhao, Chuanliu Wu · 2020 · Journal of the American Chemical Society
9. Integrating artificial intelligence with nanodiagnostics for early detection and precision management of neurodegenerative diseases
   Youssef M. Hassan, Ahmed Wanas, Ayat A. Ali, Wael Mohamed El-Sayed · 2025 · Journal of Nanobiotechnology
10. New Modalities, Technologies, and Partnerships in Probe and Lead Generation: Enabling a Mode-of-Action Centric Paradigm
    Eric Valeur, Patrick Jimonet · 2018 · Journal of Medicinal Chemistry
11. Rapid prototyping of proteins: Mail order gene fragments to assayable proteins within 24 hours
    Jared Lynn Dopp, Samuel Michael Rothstein, Thomas J. Mansell, Nigel Forest Reuel · 2018 · Biotechnology and Bioengineering
12. Design of Protein Segments and Peptides for Binding to Protein Targets
    Suchetana Gupta, Noora Azadvari, Parisa Hosseinzadeh · 2022 · BioDesign Research
13. Transferrin receptor targeting by de novo sheet extension
    Danny D. Sahtoe, Adrian Coscia, Nur Mustafaoğlu, Lauren M. Miller, Daniel Olal, Ivan Vulovic, Ta-Yi Yu, Inna Goreshnik, Yu‐Ru Lin, Lars E. Clark et al. · 2021 · Proceedings of the National Academy of Sciences
14. Neutralizing Antibodies Targeting the Conserved Stem Region of Influenza Hemagglutinin
    Sabari Nath Neerukonda, Russell A. Vassell, Carol D. Weiss · 2020 · Vaccines
15. Peptide-nanoparticle conjugates as a theranostic platform
    Suhyeon Kim, Young Hyun No, Ronald Sluyter, Konstantin Konstantinov, Jung Ho Kim, Jung Ho Kim · 2023 · Coordination Chemistry Reviews
16. CXC-Mediated Cellular Uptake of Miniproteins: Forsaking “Arginine Magic”
    Xiaoting Meng, Tao Li, Yibing Zhao, Chuanliu Wu · 2018 · ACS Chemical Biology
17. Rosetta FunFolDes – A general framework for the computational design of functional proteins
    Jaume Bonet, Sarah Wehrle, Karen Schriever, Che Yang, Anne Billet, Fabian Sesterhenn, Andreas Scheck, Freyr Sverrisson, Barbora Veselková, Sabrina S. Vollers et al. · 2018 · PLoS Computational Biology
18. Targeting overexpressed antigens in glioblastoma via CAR T cells with computationally designed high-affinity protein binders
    Zhen Xia, Qihan Jin, Zhilin Long, Yexuan He, Fuyi Liu, Chengfang Sun, Jinyang Liao, Chun Wang, Chentong Wang, Jian Zheng et al. · 2024 · Nature Biomedical Engineering
19. Nanoreactor Design Based on Self-Assembling Protein Nanocages
    Huimei Ren, Shaozhou Zhu, Guojun Zheng · 2019 · International Journal of Molecular Sciences
20. Prospects of Neutralizing Nanobodies Against SARS-CoV-2
    Fangfang Chen, Zhihong Liu, Fan Jiang · 2021 · Frontiers in Immunology
21. Quantifying the nativeness of antibody sequences using long short-term memory networks
    Andrew M. Wollacott, Chonghua Xue, Qiuyuan Qin, June Hua, Tanggis Bohnuud, Karthik Viswanathan, Vijaya B. Kolachalama · 2019 · Protein Engineering Design and Selection
22. Structural Insights into Rational Design of Single-Domain Antibody-Based Antitoxins against Botulinum Neurotoxins
    Kwok Ho Lam, Jacqueline M. Tremblay, Edwin J Vazquez-Cintron, Kay Perry, Celinia A. Ondeck, Robert P. Webb, Patrick Michael McNutt, Charles B. Shoemaker, Rongsheng Jin · 2020 · Cell Reports
23. Using AlphaFold for Rapid and Accurate Fixed Backbone Protein Design
    Moffat, Lewis, Greener, Joe G., Jones, David T. · 2021
24. Computational protein design — the next generation tool to expand synthetic biology applications
    Pablo Gainza-Cirauqui, Bruno Emanuel Correia · 2018 · Current Opinion in Biotechnology
25. Intrinsic Nucleotide Preference of Diversifying Base Editors Guides Antibody Ex Vivo Affinity Maturation
    Liu Daisy Liu, Min Huang, Pengfei Dai, Tingting Liu, Shuangshuang Fan, Xueqian Cheng, Yaofeng Zhao, Leng-Siew Yeap, Fei‐Long Meng · 2018 · Cell Reports
26. Robust folding of a de novo designed ideal protein even with most of the core mutated to valine
    Rie Koga, Mami Yamamoto, Takahiro Kosugi, Naohiro Kobayashi, Toshihiko Sugiki, Toshimichi Fujiwara, Nobuyasu Koga · 2020 · Proceedings of the National Academy of Sciences
27. The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling
    Lily Wang, Pavan Kumar Behara, Matthew W. Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey Wagner, Daniel J. Cole, Michael K. Gilson, Michael R. Shirts, David L. Mobley · 2024 · The Journal of Physical Chemistry B
28. Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein
    Sujit Basak, R. Paul Nobrega, Davide Tavella, Laura M. Deveau, Nobuyasu Koga, Rie Koga, David A. Baker, Francesca Massi, C. Robert Matthews · 2019 · Proceedings of the National Academy of Sciences
29. Comparison of Rosetta flexible‐backbone computational protein design methods on binding interactions
    Amanda L. Loshbaugh, Tanja Kortemme · 2019 · Proteins Structure Function and Bioinformatics
30. Creating Red Light-Switchable Protein Dimerization Systems as Genetically Encoded Actuators with High Specificity
    Zhimin Huang, Zengpeng Li, Xiao Zhang, Shoukai Kang, Runze Dong, Li Sun, Xiaonan Fu, David Vaisar, Kurumi Watanabe, Liangcai Gu · 2020 · ACS Synthetic Biology
31. Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset
    Simon K. S. Chu, Kush Narang, Justin B. Siegel · 2024 · PLoS Computational Biology
32. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification
    Leng-Siew Yeap, Fei‐Long Meng · 2019 · Advances in immunology
33. Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations
    Emilia Pecora de Barros, Jamie M. Schiffer, Anastassia Andreevna Vorobieva, Jiayi Dou, David A. Baker, Rommie E. Amaro · 2019 · Journal of Chemical Theory and Computation
34. ACE2‐based decoy receptors for SARS coronavirus 2
    Wenyang Jing, Erik Procko · 2021 · Proteins Structure Function and Bioinformatics
35. Design of proteins presenting discontinuous functional sites using deep learning
    Doug Tischer, Sidney Lyayuga Lisanza, Jue Wang, Runze Dong, Ivan V. Anishchenko, Lukas F. Milles, Sergey Ovchinnikov, David A. Baker · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
36. How can we improve peptide drug discovery? Learning from the past
    David J. Craik, Meng‐Wei Kan · 2021 · Expert Opinion on Drug Discovery
37. Construction of supramolecular nanotubes from protein crystals
    T. K. Nguyen, H. Negishi, S. Abe, T. Ueno · 2018 · Chemical Science
38. Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen
    Fabian Sesterhenn, Marie Galloux, Sabrina S. Vollers, Lucia Csepregi, Che Yang, Delphyne Descamps, Jaume Bonet, Simon Friedensohn, Pablo Gaínza, Patricia Corthésy et al. · 2019 · PLoS Biology
39. Exploration of novel αβ-protein folds through de novo design
    Shintaro Minami, Naohiro Kobayashi, Toshihiko Sugiki, Toshio Nagashima, Toshimichi Fujiwara, Rie Koga, George Chikenji, Nobuyasu Koga · 2023 · Nature Structural & Molecular Biology
40. The advent of de novo proteins for cancer immunotherapy
    Alfredo Quijano‐Rubio, Umut Y. Ulge, Carl Walkey, Daniel‐Adriano Silva · 2020 · Current Opinion in Chemical Biology
41. Insights into protein structure, stability and function from saturation mutagenesis
    Kritika Gupta, Raghavan Varadarajan · 2018 · Current Opinion in Structural Biology
42. Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1
    Vincent Frappier, Justin M. Jenson, Jianfu Zhou, Gevorg Grigoryan, Amy E. Keating · 2019 · Structure
43. Accurate de novo design of heterochiral protein–protein interactions
    Ke Sun, Sicong Li, Bowen Zheng, Yanlei Zhu, Tongyue Wang, Mingfu Liang, Yue Yao, Kairan Zhang, Jizhong Zhang, Hongyong Li et al. · 2024 · Cell Research
44. Design of high-affinity binders to immune modulating receptors for cancer immunotherapy
    Wei Yang, Derrick R. Hicks, Agnidipta Ghosh, Tristin A. Schwartze, Brian Coventry, Inna Goreshnik, Aza Allen, Samer F. Halabiya, Chan Johng Kim, Cynthia S. Hinck et al. · 2025 · Nature Communications
45. Designed for life: biocompatible de novo designed proteins and components
    Katie J. Grayson, J. L. Ross Anderson · 2018 · Journal of The Royal Society Interface
46. Solution thermochemistry of concanavalin A tetramer conformers measured by variable-temperature ESI-IMS-MS
    Tarick J. El‐Baba, David E. Clemmer · 2019 · International Journal of Mass Spectrometry
47. Large-scale design and refinement of stable proteins using sequence-only models
    Jedediah M. Singer, Scott Novotney, Devin Strickland, Hugh K. Haddox, Nicholas Leiby, Gabriel J. Rocklin, Cameron M. Chow, Anindya Roy, Asim K. Bera, Francis C. Motta et al. · 2022 · PLoS ONE
48. De novo design of protein minibinder agonists of TLR3
    Chloe S. Adams, Hyojin Kim, Abigail E. Burtner, Dong Sun Lee, Craig Dobbins, Cameron Criswell, Brian Coventry, Adri Tran-Pearson, Ho Min Kim, Neil P. King · 2025 · Nature Communications
49. Hierarchical design of artificial proteins and complexes toward synthetic structural biology
    Ryoichi Arai · 2017 · Biophysical Reviews
50. Bispecific applications of non-immunoglobulin scaffold binders
    Sophia Hober, Sarah Lindbo, Johan Nilvebrant · 2018 · Methods
51. Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity
    Brandon Havranek, Kui K. Chan, Austin Wu, Erik Procko, Shahidul M. Islam · 2021 · Journal of Chemical Information and Modeling
52. Solubility-Aware Protein Binding Peptide Design Using AlphaFold
    Takatsugu Kosugi, Masahito Ohue · 2022 · Biomedicines
53. Protein‐Based Controllable Nanoarchitectonics for Desired Applications
    Ling Li, Yingying Zhang, Yage Wu, Zhengge Wang, Wandi Cui, Chunhong Zhang, Jinglin Wang, Yongchun Liu, Peng Yang · 2024 · Advanced Functional Materials
54. Dual-Readout Sandwich Immunoassay for Device-Free and Highly Sensitive Anthrax Biomarker Detection
    Isaac N. Larkin, G. Viswanadham, Gokay Yamankurt, Alexander W. Scott, Hang Xing, Chad Alexander Mirkin · 2020 · Analytical Chemistry
55. De novo design of a transcription factor for a progesterone biosensor
    Kun Liu, Yunsen Zhang, Ke Liu, Yunqiu Zhao, Bei Gao, Xinyi Tao, Ming Zhao, Feng‐Qing Wang, Dongzhi Wei · 2021 · Biosensors and Bioelectronics
56. Chimeric antigen receptor Treg therapy in transplantation
    Siawosh K. Eskandari, Andrea Daccache, Jamil R. Azzi · 2023 · Trends in Immunology
57. Better together: building protein oligomers naturally and by design
    Rebecca E. A. Gwyther, D. Dafydd Jones, Harley L. Worthy · 2019 · Biochemical Society Transactions
58. Design in the DARK: Learning Deep Generative Models for De Novo Protein Design
    Moffat, Lewis, Kandathil, Shaun M., Jones, David T. · 2022
59. Recent advances in automated protein design and its future challenges
    Setiawan, Dani, Brender, Jeffrey, Zhang, Yang · 2018 · Expert Opinion on Drug Discovery
60. Peptide design through binding interface mimicry with PepMimic
    2025
61. Synthetic transcription factor engineering for cell and gene therapy
    Bhoomi Bhatt, Pablo García-Díaz, G. Wink · 2023 · Trends in biotechnology
62. The ascent of man(made oxidoreductases)
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63. Design of complicated all-α protein structures
    Koya Sakuma, Naohiro Kobayashi, Toshihiko Sugiki, Toshio Nagashima, Toshimichi Fujiwara, Kano Suzuki, Naoya Kobayashi, Takeshi Murata, Takahiro Kosugi, Rie Koga et al. · 2024 · Nature Structural & Molecular Biology
64. Peptide-targeted nanoparticles for tumor therapy
    Valeria Sidorenko, Allan Tobi, Kazuki N. Sugahara, Tambet Teesalu · 2025 · Journal of Controlled Release
65. Positive functional synergy of structurally integrated artificial protein dimers assembled by Click chemistry
    Harley L. Worthy, Husam Sabah Auhim, William David Jamieson, Jacob R. Pope, Aaron Wall, Robert H. Batchelor, Rachel L. Johnson, Daniel W. Watkins, P.J. Rizkallah, Oliver Kieran Castell et al. · 2019 · Communications Chemistry
66. Structure-guided design of CPPC-paired disulfide-rich peptide libraries for ligand and drug discovery
    Yapei Wu, Shihui Fan, Dong Meng, Jinjing Li, Chuilian Kong, Jie Zhuang, Xiaoting Meng, Shuaimin Lu, Yibing Zhao, Chuanliu Wu · 2022 · Chemical Science
67. Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition
    Tudor‐Stefan Cotet, Igor Krawczuk, Filippo Stocco, Noelia Ferruz, Anthony Gitter, Yoichi Kurumida, Lucas de Almeida Machado, Francesco Paesani, Cianna N. Calia, Chance A. Challacombe et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
68. A mini-review and perspective on multicyclic peptide mimics of antibodies
    Weidong Liu, Chuanliu Wu · 2018 · Chinese Chemical Letters
69. Resolving overlapped signals with automated FitNMR analytical peak modeling
    Joshua A. Dudley, Sojeong Park, Meagan E. MacDonald, Fetene Emanual, Colin A. Smith · 2020 · Journal of Magnetic Resonance
70. Arming Yourself for The In Silico Protein Design Revolution
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71. Prediction of Residue-specific Contributions to Binding and Thermal Stability Using Yeast Surface Display
    Shahbaz Ahmed, Munmun Bhasin, Kavyashree Manjunath, Raghavan Varadarajan · 2022 · Frontiers in Molecular Biosciences
72. Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation
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73. Approaches to the Structure-Based Design of Antivirulence Drugs: Therapeutics for the Post-Antibiotic Era
    Nolan Neville, Zongchao Jia · 2019 · Molecules
74. Data-driven engineering of protein therapeutics
    Matthew S. Faber, Timothy A. Whitehead · 2019 · Current Opinion in Biotechnology
75. The plasticity of redox cofactors: from metalloenzymes to redox-active DNA
    Anja Hemschemeier, Thomas Happe · 2018 · Nature Reviews Chemistry
76. Comparison of α-Helix and β-Sheet Structure Adaptation to a Quantum Dot Geometry: Toward the Identification of an Optimal Motif for a Protein Nanoparticle Cover
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77. Computational design of SARS-CoV-2 peptide binders with better predicted binding affinities than human ACE2 receptor
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78. Assessing and enhancing foldability in designed proteins
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79. Computational Protein Design for COVID-19 Research and Emerging Therapeutics
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80. Design Strategy to Create Antibody Mimetics Harbouring Immobilised Complementarity Determining Region Peptides for Practical Use
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81. Molecular Dynamic Simulations and Molecular Docking as a Potential Way for Designed New Inhibitor Drug without Resistance.
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82. A Dynamic Hydrophobic Core and Surface Salt Bridges Thermostabilize a Designed Three-Helix Bundle
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83. Importance of interface and surface areas in protein-protein binding affinity prediction: A machine learning analysis based on linear regression and artificial neural network
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84. Miniproteins in medicinal chemistry
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85. De novo design of mini-protein binders broadly neutralizing Clostridioides difficile toxin B variants
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86. High-throughput identification of dominant negative polypeptides in yeast
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87. Peptide-Based Nanomaterials for Tumor Immunotherapy
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88. Design and Engineering of Miniproteins
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89. Computational modeling and prediction of deletion mutants
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90. The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes
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91. A generic framework for hierarchical de novo protein design
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92. Motif-Directed Oxidative Folding to Design and Discover Multicyclic Peptides for Protein Recognition
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93. Designing Short Peptides to Block the Interaction of SARS-CoV-2 and Human ACE2 for COVID-19 Therapeutics
    Abdul Basit, Asad Mustafa Karim, Muhammad Asif, Tanveer Ali, Jung Hun Lee, Jeong Ho Jeon, Shafiq ur Rehman, Sang Hee Lee · 2021 · Frontiers in Pharmacology
94. Tailored Functionalized Protein Nanocarriers for Cancer Therapy: Recent Developments and Prospects
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95. Combining Rational Design and Continuous Evolution on Minimalist Proteins That Target the E-box DNA Site
    Ichiro Inamoto, Inder Singh Sheoran, Serban C. Popa, Montdher Hussain, Jumi A. Shin · 2020 · ACS Chemical Biology
96. Principles and Methods in Computational Membrane Protein Design
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97. Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically‐Encoded Probes for DNA‐PAINT
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98. Protein scaffolds in human clinics
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99. Adaption of human antibody λ and κ light chain architectures to CDR repertoires
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100. PARCE: Protocol for Amino acid Refinement through Computational Evolution
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