ArticleScience (New York, N.Y.)2023
Deploying synthetic coevolution and machine learning to engineer protein-protein interactions.
Article in Science (New York, N.Y.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Antibody Affinity Maturation by Yeast Mating against a Diverse Antigen Library Enhances Antibody Resistance to Viral Mutations.ACS pharmacology & translational science · 2026Article
- High-throughput measurements of protein domain functions using magnetic separation.Nature protocols · 2026Review
- Design of strictly orthogonal biosensors for maximizing renewable biofuel overproduction.Journal of advanced research · 2026Article
- The evolution of display technologies for antibody drug discovery.Trends in biotechnology · 2026Review
- Structural ontogeny of protein-protein interactions.Science (New York, N.Y.) · 2026Article
- Screening and machine learning-based prediction of translation-enhancing peptides that reduce ribosomal stalling inRSC chemical biology · 2026Article
- Predicting Protein-Protein Interactions from Machine-Learned Representations.Advances in experimental medicine and biology · 2026Review
- Library-on-Library Intercellular Labeling for Selection of Biotin Ligase and Acceptor Peptides.Chembiochem : a European journal of chemical biology · 2026Article
- Comparing Neural Networks and Naive Bayes in the Prediction of Drug Gene Interactions of Type 4 Collagenase for Gingival Epithelialization.International journal of dentistry · 2026Article
- UV-B Responsive Flavonoid Synthesis Contributes to Tartary Buckwheat High-Altitude Adaption.Plant biotechnology journal · 2025Article
- Evolutionary paths that link orthogonal pairs of binding proteins.Cell systems · 2025Article
- Synthetic biology and artificial intelligence in crop improvement.Plant communications · 2025Review
- TPepPro: a deep learning model for predicting peptide-protein interactions.Bioinformatics (Oxford, England) · 2024Article
- Expanding the landscape of antibody discovery.Cell reports methods · 2024Article
- Graph Neural Networks-Based Prediction of Drug Gene Interactions of RTK-VEGF4 Receptor Family in Periodontal Regeneration.Journal of clinical and experimental dentistry · 2024Article
- Reactive Oxygen Species Mechanisms that Regulate Protein-Protein Interactions in Cancer.International journal of molecular sciences · 2024Review
- Addressing epistasis in the design of protein function.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Computational tools for plant genomics and breeding.Science China. Life sciences · 2024Review
- Assessing the functional roles of coevolving PHD finger residues.Protein science : a publication of the Protein Society · 2024Article
- A library-on-library screen reveals the breadth expansion landscape of a broadly neutralizing betacoronavirus antibody.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain-affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pretrained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. The integration of these approaches provides a means of simulating protein coevolution and generating protein complexes with diverse molecular recognition properties for biotechnology and synthetic biology.
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Registered trials
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