An evolution-based model for designing chorismate mutase enzymes

Cited by (314)

Items 101–200 of 314

1. Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes
   Lucile Vigué, Giancarlo Croce, Marie Petitjean, Étienne Ruppé, Olivier Tenaillon, Martin Weigt · 2022 · Nature Communications
2. Inferring protein fitness landscapes from laboratory evolution experiments
   Sameer D’Costa, Emily C. Hinds, Chase R. Freschlin, Hyebin Song, Philip A. Romero · 2023 · PLoS Computational Biology
3. Understanding epistatic networks in the B1 β-lactamases through coevolutionary statistical modeling and deep mutational scanning
   John Z. Chen, Matteo Bisardi, D. Lee, Sabrina Cotogno, Francesco Zamponi, Martin Weigt, Nobuhiko Tokuriki · 2024 · Nature Communications
4. Optimal Design of Stochastic DNA Synthesis Protocols based on Generative Sequence Models
   Eli N. Weinstein, Alan N. Amin, Will Grathwohl, Daniel Kassler, Jean Disset, Debora S. Marks · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
5. ProtWave-VAE: Integrating Autoregressive Sampling with Latent-Based Inference for Data-Driven Protein Design
   Praljak, Nikša, Lian, Xinran, Ranganathan, Rama, Ferguson, Andrew L. · 2023 · ACS Synthetic Biology
6. Aligning biological sequences by exploiting residue conservation and coevolution
   Anna Paola Muntoni, Andrea Pagnani, Martin Weigt, Francesco Zamponi · 2020 · Physical review. E
7. Reduced B cell antigenicity of Omicron lowers host serologic response
   Jérôme Tubiana, Yufei Xiang, Li Fan, Haim J. Wolfson, Kong Chen, Dina Schneidman‐Duhovny, Yi Shi · 2022 · Cell Reports
8. ProtMamba: a homology-aware but alignment-free protein state space model
   Sgarbossa, Damiano, Malbranke, Cyril, Bitbol, Anne-Florence · 2025 · Bioinformatics
9. Cutting-edge computational approaches in enzyme design and activity enhancement
   Ruobin Sun, Dan Wu, Pengcheng Chen, Pu Zheng · 2024 · Biochemical Engineering Journal
10. High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing
    Kuang‐Yu Chen, Jayaprakash Karuppusamy, Mary B. O’Neill, Vaitea Opuu, Mathieu Bahin, Sophie Foulon, Pablo Ibanez, Lluís Quintana‐Murci, Tatsuhiko Ozawa, Sylvie van der Werf et al. · 2023 · Proceedings of the National Academy of Sciences
11. Leri: A web-server for identifying protein functional networks from evolutionary couplings
    Ngaam J. Cheung, Arun T. John Peter, Benoı̂t Kornmann · 2021 · Computational and Structural Biotechnology Journal
12. Machine learning meets enzyme engineering: examples in the design of polyethylene terephthalate hydrolases
    Rohan Ali, Yifei Zhang · 2024 · Frontiers of Chemical Science and Engineering
13. Residue conservation and solvent accessibility are (almost) all you need for predicting mutational effects in proteins
    Tsishyn, Matsvei, Hermans, Pauline, Rooman, Marianne, Pucci, Fabrizio · 2025 · Bioinformatics
14. Generating novel protein sequences using Gibbs sampling of masked language models
    Sean R. Johnson, Sarah Monaco, Kenneth Massie, Zaid Syed · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
15. Exploring the Protein Sequence Space with Global Generative Models
    Sergio Romero‐Romero, Sebastian Lindner, Noelia Ferruz · 2023 · Cold Spring Harbor Perspectives in Biology
16. Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment
    Malbranke, Cyril, Rostain, William, Depardieu, Florence, Cocco, Simona, Monasson, Rémi, Bikard, David · 2023 · PLOS Computational Biology
17. Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics
    2025
18. Scalable and cost-efficient custom gene library assembly from oligopools
    Chase R. Freschlin, Kevin K. Yang, Philip A. Romero · 2026 · Science Advances
19. Modulating Glycoside Hydrolase Activity between Hydrolysis and Transfer Reactions Using an Evolutionary Approach
    Rodrigo Arreola-Barroso, Alexey Llopiz, Leticia Olvera, Gloria Saab‐Rincón · 2021 · Molecules
20. Variational autoencoder for design of synthetic viral vector serotypes
    Suyue Lyu, Shahin Sowlati‐Hashjin, Michael Garton · 2024 · Nature Machine Intelligence
21. Molecular flexibility in computational protein design: an algorithmic perspective
    Younes Bouchiba, Juan Cortés, Thomas Schiex, Sophie Barbe · 2021 · Protein Engineering Design and Selection
22. Now What Sequence? Pre-trained Ensembles for Bayesian Optimization of Protein Sequences
    Ziyue Yang, Katarina A. Milas, Andrew D. White · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
23. Relation Between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions
    Raimundo Saona, Fyodor A. Kondrashov, Ksenia A. Khudiakova · 2022 · Bulletin of Mathematical Biology
24. On the role of native contact cooperativity in protein folding
    David Wang, Layne B. Frechette, Robert B. Best · 2024 · Proceedings of the National Academy of Sciences
25. Machine learning in biological physics: From biomolecular prediction to design
    Jonathan Martin, M. Mateos, José N. Onuchic, Ivan Coluzza, Faruck Morcos · 2024 · Proceedings of the National Academy of Sciences
26. Statistical mechanics for networks of real neurons
    Leenoy Meshulam, William Bialek · 2025 · Reviews of Modern Physics
27. Design of a Protein with Improved Thermal Stability by an Evolution‐Based Generative Model
    Pengfei Tian, Adrien Lemaire, Fabien Sénéchal, Olivier Habrylo, Viviane Antonietti, Pascal Sonnet, Valérie Lefebvre, Frederikke Isa Marin, Robert B. Best, Jérôme Pelloux et al. · 2022 · Angewandte Chemie International Edition
28. Exploring Large Protein Sequence Space through Homology- and Representation-based Hierarchical Clustering
    John Z. Chen, B. Gall, S. B. Pulsford, N. Tokuriki, Colin J Jackson · 2025 · Molecular biology and evolution
29. Illuminating the universe of enzyme catalysis in the era of artificial intelligence
    Jason Yang, Francesca-Zhoufan Li, Yueming Long, Frances H. Arnold · 2025 · Cell Systems
30. Functional effects of mutations in proteins can be predicted and interpreted by guided selection of sequence covariation information
    Simona Cocco, Lorenzo Posani, Rémi Monasson · 2024 · Proceedings of the National Academy of Sciences
31. Biochemical and Computational Characterization of Haloalkane Dehalogenase Variants Designed by Generative AI: Accelerating the SN2 Step
    Natalia Gelfand, Vojtěch Orel, Wenqiang Cui, Jiřı́ Damborský, Chenglong Li, Zbyněk Prokop, Wen Jun Xie, Arieh Warshel · 2025 · Journal of the American Chemical Society
32. Reconstruction of Ancestral Protein Sequences Using Autoregressive Generative Models
    Matteo De Leonardis, Andrea Pagnani, Pierre Barrat-Charlaix · 2024 · bioRxiv
33. Evolving the naturally compromised chorismate mutase from Mycobacterium tuberculosis to top performance
    Jūratė Fahrig‐Kamarauskaitė, Kathrin Würth-Roderer, Helen V. Thorbjørnsrud, Susanne Mailand, Ute Krengel, Peter Kast · 2020 · Journal of Biological Chemistry
34. Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences
    2022
35. Tractable Regularization of Probabilistic Circuits
    Anji Liu, Guy Van den Broeck · 2021 · arXiv (Cornell University)
36. Sequence grammar underlying unfolding and phase separation of globular proteins
    Kiersten M. Ruff, Yoon Hee Choi, Dezerae Cox, Angelique R. Ormsby, Yoochan Myung, David Benjamin Ascher, Sheena E. Radford, Rohit V. Pappu, Danny M. Hatters · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
37. Undersampling and the inference of coevolution in proteins
    Yaakov Kleeorin, William P. Russ, Olivier Rivoire, Rama Ranganathan · 2023 · Cell Systems
38. Towards parsimonious generative modeling of RNA families
    Francesco Calvanese, Camille N. Lambert, Philippe Nghe, Francesco Zamponi, Martin Weigt · 2024 · Nucleic Acids Research
39. Novel Insights into Enzymatic Thermostability: The “Short Board” Theory and Zero‐Shot Hamiltonian Model
    Min Liao, Shihao Feng, Xiaoqing Liu, Guoshun Xu, Sicong Li, Yingguo Bai, Huiying Luo, Bin Yao, Haobo Wang, Tao Tu · 2024 · Advanced Science
40. Exploring the space of self-reproducing ribozymes using generative models
    Camille N. Lambert, Vaitea Opuu, Francesco Calvanese, Polina Pavlinova, Francesco Zamponi, Eric J. Hayden, Martin Weigt, Matteo Smerlak, Philippe Nghe · 2025 · Nature Communications
41. Beneath the XNA world: Tools and targets to build novel biology
    Paola Handal-Marquez, Anupama Anupama, Valérie Pezo, Philippe Marlière, Piet A. Herdewijn, Vitor Bernardes Pinheiro · 2020 · Current Opinion in Systems Biology
42. Coupling a Live Cell Directed Evolution Assay with Coevolutionary Landscapes to Engineer an Improved Fluorescent Rhodopsin Chloride Sensor
    Hsichuan Chi, Qin Zhou, Jasmine N. Tutol, Shelby M. Phelps, Jessica Lee, Paarth Kapadia, Faruck Morcos, Sheel C. Dodani · 2022 · ACS Synthetic Biology
43. Mutational Paths with Sequence-Based Models of Proteins: From Sampling to Mean-Field Characterization
    Eugenio Mauri, Simona Cocco, Rémi Monasson · 2023 · Physical Review Letters
44. ProteinVAE: Variational AutoEncoder for Translational Protein Design
    Suyue Lyu, Shahin Sowlati‐Hashjin, Michael Garton · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
45. Coherent Blending of Biophysics-Based Knowledge with Bayesian Neural Networks for Robust Protein Property Prediction
    Hunter M. Nisonoff, Zhaoran Wang, Jennifer Listgarten · 2023 · ACS Synthetic Biology
46. Descriptor-augmented machine learning for enzyme-chemical interaction predictions
    Yilei Han, Hao-Ye Zhang, Zhe-Ni Zeng, Zhi-Yuan Liu, Dian-Nan Lu, Zheng Liu · 2024 · Synthetic and Systems Biotechnology
47. Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions
    Jérôme Tubiana, Lucia Adriana Lifshits, Michael Nissan, Matan Gabay, Inbal Sher, Marina Sova, Haim J. Wolfson, Maayan Gal · 2023 · PLoS Computational Biology
48. Intelligent Protein Design and Molecular Characterization Techniques: A Comprehensive Review
    Jingjing Wang, Chang Chen, Ge Yao, Junjie Ding, Liangliang Wang, Hui Jiang · 2023 · Molecules
49. A hybrid model combining evolutionary probability and machine learning leverages data-driven protein engineering
    Alexander-Maurice Illig, Niklas E. Siedhoff, Ulrich Schwaneberg, Mehdi D. Davari · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
50. Deep learning-enabled design of synthetic orthologs of a signaling protein
    Xinran Lian, Niksa Praljak, Subu K. Subramanian, Sarah Wasinger, Rama Ranganathan, Andrew L. Ferguson · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
51. A Cyanobacterial Screening Platform for Rubisco Mutant Variants
    Hoffmann, Ute A., Schuppe, Anna Z., Knave, Axel, Sporre, Emil, Brismar, Hjalmar, Englund, Elias, Syrén, Per-Olof, Hudson, Elton P. · 2025 · ACS Synthetic Biology
52. Exact minimax entropy models of large-scale neuronal activity
    Christopher W. Lynn, Qiwei Yu, Rich Pang, Stephanie E. Palmer, William Bialek · 2025 · Physical review. E
53. Impact of phylogeny on structural contact inference from protein sequence data
    Dietler, Nicola, Lupo, Umberto, Bitbol, Anne-Florence · 2023 · Journal of The Royal Society Interface
54. Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase
    Thomas J. Summers, Reza Hemmati, Justin E. Miller, Donatus A. Agbaglo, Qianyi Cheng, Nathan J. DeYonker · 2023 · The Journal of Chemical Physics
55. Enzyme redesign and genetic code expansion
    Vaitea Opuu, Thomas Simonson · 2023 · Protein Engineering Design and Selection
56. Exactly solvable statistical physics models for large neuronal populations
    Christopher W. Lynn, Qiwei Yu, Rich Pang, William Bialek, Stephanie E. Palmer · 2025 · Physical Review Research
57. Deep-learning-based design of synthetic orthologs of SH3 signaling domains
    Xinran Lian, Niksa Praljak, Subu Subramanian, Sarah Wasinger, Rama Ranganathan, Andrew L. Ferguson · 2024 · Cell Systems
58. Computational Protein Design - Where it goes?
    Binbin Xu, Yingjun Chen, Weiwei Xue · 2023 · Current Medicinal Chemistry
59. MBE: model-based enrichment estimation and prediction for differential sequencing data
    Akosua Busia, Jennifer Listgarten · 2023 · Genome biology
60. Reduced antigenicity of Omicron lowers host serologic response
    Jérôme Tubiana, Yufei Xiang, Li Fan, Haim J. Wolfson, Kong Chen, Dina Schneidman‐Duhovny, Yi Shi · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
61. Multi-Enzyme Synergy and Allosteric Regulation in the Shikimate Pathway: Biocatalytic Platforms for Industrial Applications
    Sara Khan, David D. Boehr · 2025 · Catalysts
62. Improving sequence-based modeling of protein families using secondary-structure quality assessment
    Cyril Malbranke, David Bikard, Simona Cocco, Rémi Monasson · 2021 · Bioinformatics
63. Singular value decomposition of protein sequences as a method to visualize sequence and residue space
    Autum R. Baxter‐Koenigs, Gina El Nesr, Doug Barrick · 2022 · Protein Science
64. In Vitro Enzyme Self-Selection Using Molecular Programs
    Adèle Dramé-Maigné, Rocío Espada, Giselle McCallum, Rémi Sieskind, Guillaume Gines, Yannick Rondelez · 2024 · ACS Synthetic Biology
65. A Robust Growth-Based Selection Platform to Evolve an Enzyme via Dependency on Noncanonical Tyrosine Analogues
    Suzanne C. Jansen, Clemens Mayer · 2024 · JACS Au
66. Integrating experimental feedback improves generative models for biological sequences
    Francesco Calvanese, Giovanni Peinetti, Polina Pavlinova, Philippe Nghe, Martin Weigt · 2025 · Nucleic Acids Research
67. A Multimodal Ensemble Framework for Optimal Mutant Prediction and Computational Enzyme Engineering
    Ding Luo, Huining Ji, Baodong Hu, Jinxing Cai, Kaiqi Wen, Xiaoyang Qu, Mingfeng Cao, Xinrui Zhao, Binju Wang · 2025 · Angewandte Chemie International Edition
68. Interpretable pairwise distillations for generative protein sequence models
    Christoph Feinauer, Barthelemy Meynard-Piganeau, Carlo Lucibello · 2022 · PLoS Computational Biology
69. From Statistical Physics to Data-Driven Modelling
    Simona Cocco, Rémi Monasson, Francesco Zamponi · 2022
70. Engineering gain‐of‐function mutants of a WW domain by dynamics and structural analysis
    Jin Lu, Mohammad Imtiazur Rahman, I. Can Kazan, Nicholas Ryan Halloran, Andrey A. Bobkov, Sefika Banu Ozkan, Giovanna Ghirlanda · 2023 · Protein Science
71. Unlearning regularization for Boltzmann machines
    Enrico Ventura, Simona Cocco, Rémi Monasson, Francesco Zamponi · 2024 · Machine Learning Science and Technology
72. On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins
    Edwin Rodríguez-Horta, Martin Weigt · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
73. Directed Evolution of Enzymes based on in vitro Programmable Self-Replication
    Adèle Dramé-Maigné, Rocío Espada, Giselle McCallum, Rémi Sieskind, Yannick Rondelez · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
74. PRO-LDM: Protein Sequence Generation with a Conditional Latent Diffusion Model
    Sitao Zhang, Zixuan Jiang, Rundong Huang, Shaoxun Mo, Le-Tao Zhu, Peiheng Li, Ziyi Zhang, Emily Pan, Xi Chen, Yun-Fei Long et al. · 2024 · bioRxiv
75. Statistical design of a synthetic microbiome that suppresses diverse gut pathogens
    Rita A. Oliveira, Emma McSpadden, Bipul Pandey, Kiseok Keith Lee, Mahmoud Yousef, Robert Yuzen Chen, Conrad Triebold, Fidel Haro, Valeryia Aksianiuk, Riya Patel et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
76. Fluctuations and the limit of predictability in protein evolution
    Saverio Rossi, Leonardo Di Bari, Martin Weigt, Francesco Zamponi · 2025 · Reports on Progress in Physics
77. Design of SC PEP with enhanced stability against pepsin digestion and increased activity by machine learning and structural parameters modeling
    Bin Xiao, Chun Zhang, Junxiu Zhou, Sa Wang, Huan Meng, Miao Wu, Yongxiang Zheng, Rong Yu · 2023 · International Journal of Biological Macromolecules
78. Sequence-Based Protein Design: A Review of Using Statistical Models to Characterize Coevolutionary Traits for Developing Hybrid Proteins as Genetic Sensors
    Sahaj Kinshuk, Lin Li, Brian Meckes, Clement T. Y. Chan · 2024 · International Journal of Molecular Sciences
79. Data-driven design of orthogonal protein-protein interactions
    Duccio Malinverni, M. Madan Babu · 2023 · Science Signaling
80. pycofitness—Evaluating the fitness landscape of RNA and protein sequences
    Fabrizio Pucci, Mehari B. Zerihun, Marianne J. Rooman, Alexander H. Schug · 2024 · Bioinformatics
81. Global multivariate model learning from hierarchically correlated data
    Edwin Rodríguez-Horta, Alejandro Lage-Castellanos, Martin Weigt, Pierre Barrat-Charlaix · 2021 · Journal of Statistical Mechanics Theory and Experiment
82. Cracking the Metabolic engineering of bacteria: Review of methods involved in organic acid Production
    Manam Walait, Huda Rehman Mir, Zainab A. Abdel Hassan, Javed Iqbal Wattoo · 2021 · Natural Resources for Human Health
83. Generating interacting protein sequences using domain-to-domain translation
    Barthelemy Meynard-Piganeau, Caterina Fabbri, Martin Weigt, Andrea Pagnani, Christoph Feinauer · 2023 · Bioinformatics
84. Manufacturing-Aware Generative Model Architectures Enable Biological Sequence Design and Synthesis at Petascale
    Eli N. Weinstein, Mattia G. Gollub, Andrei Slabodkin, Cameron L. Gardner, Kerry Dobbs, Xiao-Bing Cui, Alan N. Amin, George McDonald Church, Elizabeth Wood · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
85. Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis
    Shukla, Divyanshu, Martin, Jonathan, Morcos, Faruck, Potoyan, Davit A. · 2025 · Journal of Chemical Theory and Computation
86. An iterative deep learning-guided algorithm for directed protein evolution
    Xiaofan Li, Qihan Wang, Jianfeng Li, Fangfang Tang, Xiaofeng Yang, Zhanglin Lin · 2025 · iScience
87. Designing a mesoporous cascade reactor for enhanced enzymatic performance
    Ziman Chen, Qunfeng Fan, Jianhua Wang, Jiyuan Zhang, Yahui Zhang, Tianwei Tan, Yongqin Lv · 2025 · Bioresource Technology
88. An industrial automated laboratory for programmable protein evolution
    Da Shen, Xin Wang, Yuan Hong Gao, Wei Wang, Yuchao Li, He Chen, Yushuai Guo, Shuaihua Cao, Y Huang, Yan Zhang et al. · 2025 · Nature Chemical Engineering
89. Minimax entropy: The statistical physics of optimal models
    David P. Carcamo, Nicholas Weaver, Purushottam D. Dixit, Christopher W. Lynn · 2025 · Physical review. E
90. A comprehensive survey on artificial intelligence for biomolecule design
    Guang Yang, Jianing Li, Qiong Wang, Lianlian Wu, Zhengshan Chen, Peng-Cheng Zhao, Haoyang Wang, Qinglong Wang, Bing Wen, Chao Song et al. · 2026 · The Innovation Life
91. Transition paths in Potts-like energy landscapes: General properties and application to protein sequence models
    Eugenio Mauri, Simona Cocco, Rémi Monasson · 2023 · Physical review. E
92. PyCoM: a python library for large-scale analysis of residue–residue coevolution data
    Philipp E Glass, Sabriyeh Alibai, Alessandro Pandini, Sarath Chandra Dantu · 2024 · Bioinformatics
93. Navigating the amino acid sequence space between functional proteins using a deep learning framework
    Tristan Bitard-Feildel · 2021 · PeerJ Computer Science
94. A generative nonparametric Bayesian model for whole genomes
    Alan N. Amin, Eli N. Weinstein, Debora S. Marks · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
95. Mean Dimension of Generative Models for Protein Sequences
    Christoph Feinauer, Emanuele Borgonovo · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
96. FLOP: Tasks for Fitness Landscapes Of Protein wildtypes
    Peter Mørch Groth, Michaël Richard, Jesper Salomon, Pengfei Tian, Wouter Boomsma · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
97. Contrastive Fitness Learning: Reprogramming Protein Language Models for Low- N Learning of Protein Fitness Landscape
    Junming Zhao, Chao Zhang, Yunan Luo · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
98. Natural Language Prompts Guide the Design of Novel Functional Protein Sequences
    Niksa Praljak, Hugh Yeh, Miranda Moore, Michael Socolich, Rama Ranganathan, Andrew L. Ferguson · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
99. Inference and visualization of complex genotype-phenotype maps with gpmap-tools
    Carlos Martí-Gómez, Juan-Nan Zhou, Wei-Chia Chen, A. Stoltzfus, J. Kinney, David M. McCandlish · 2025 · bioRxiv
100. Combinatorial assembly and design of enzymes
     Lipsh-Sokolik, Rosalie, Khersonsky, Olga, Schröder, Sybrin P., de Boer, Casper, Hoch, Shlomo-Yakir, Davies, Gideon J., Overkleeft, Hermen S., Fleishman, Sarel J. · 2022